Public Access

As a service to the community, CDD hosts Public Access Data relevant to drug discovery from leading research groups around the world.

Fully integrated with the CDD Vault, users have full access to these sets directly from their accounts. Scientists without CDD Vault access who wish to view or mine our repository of Public Access Data can register for a free account. We welcome and encourage contributions. Scientists who wish to publish to CDD Public should contact us.

Title Published By Molecules


PI: Tassie Collins
Published: 10/21/2016
Myelin Repair Foundation 710
Acute Oligodendrocyte differentiation assay O4 immunopurified OPCs were plated at 5k/well. 1 hr after plating, test article was added and cells were incubated for four days, whereupon cells were fixed and immunostained for MBP and total nuclei (DAPI). OPC differentiation into OLs was determined by quantification of MBP staining/number of cells (identified by DAPI nuclear staining). Screening of compounds was performed in quadruplicate at 2 concentrations (10 & 2 uM; 2 & 0.4 uM; 0.4 & 0.08 uM). Data are normalized to DMSO (0% differentiation) and 40 ng/ml T3 (100% differentiation). EC50 is determined relative to the EMax of the test article. For technical details see Lariosa-Willingham, et. , al, BMC Res Notes. 2016 Sep 5;9(1):419 or contact [email protected] for detailed protocols.


PI: Tassie Collins
Published: 10/21/2016
Myelin Repair Foundation 723
Oligodendrocyte Protection Assay – Viability (TNF+IFNg) Expanded OPCs were plated at 10K/well. 24 hrs after plating, test article was added, 1hr after test article addition, insult with 10U/ml IFN-gamma/1ng/ml TNF-alpha was added. Incubate 2 days, add AlamarBlue and incubate four hrs. Quantify AlamarBlue fluorescence to read out cellular viability. Data are scaled to DMSO (0% activity) and 1.1 uM quetiapine (100% activity). For technical details see Rosler, et. , al, BMC Res Notes. 2016 Sep 5;9(1):444 contact [email protected] for detailed protocols.


PI: Tassie Collins
Published: 10/21/2016
Myelin Repair Foundation 715
Cortical Myelination Assay Cells from E18 brain cortex were prepared and plated in Neuralbasal media. Four days later, media was switched to MyM media. On day 5, test articles are added and myelination allowed to proceed for eight days. On day 13 in vitro, cells were fixed and immunostained for MBP and Olig2. Myelination was determined by quantification of MBP/Olig2+ nuclei staining and change of MBP morphology (alignment of contiguous MBP staining – fiber length). OL differentiation was determined by quantification of the MBP density x area/Olig2+ nuclei. Compounds were screened in duplicate with 4 images/well at 2 concentrations (5 & 1 uM). Data are normalized to DMSO (0% differentiation/myelination) and DAPT (100% differentiation/myelination). EC50s determined relative to response to 1 uM DAPT. For technical details see Lariosa-Willingham, et. , al, BMC Neurosci. 2016 Apr 22;17:16 or contact [email protected] for detailed protocols.

MULTIPLE SCLEROSIS: HEK293 tunicamycin protection assay

PI: Tassie Collins
Published: 10/7/2016
Myelin Repair Foundation 740
HEK-293 protection Assay

HEK-293 cells (10K/well) are incubated for 24 hours, then test article is added. After 1 hour, 100 ng/ml tunicamycin is added. After an additional 48-hour incubation, AlamarBlue is added and fluorescence is quantified 4 hours later. Data are normalized to DMSO (0% activity) and 5 uM guanabenz (100% activity). EC50 is determined relative to the EMax of the test article. Contact [email protected] for detailed protocols.


PI: Tassie Collins
Published: 10/7/2016
Myelin Repair Foundation 709
Oligodendrocyte Toxicity Assay (TNF+IFNg)

Toxicity assay on passaged rat OPCs, plated at 10k/well incubated with drug for 2 days. Readout is AlamarBlue fluorescence after 4 hr incubation. Data are shown as percent survival relative to DMSO (100%). Max killing is with 5 ng/ml tunicamycin, which leaves ~15% cells alive. For technical details see Lariosa-Willingham, et., al, BMC Res Notes. 2016 Sep 5;9(1):419 or contact [email protected] for detailed protocols.

Green Solvents

Published: 9/20/2016
Alex Clark Sandbox 117
Green Solvents data, used by the eponymous mobile app ( Compiled from information published by the ACS Green Chemical Institute and GSK Solvent Guide. Published in

PARASITES: GSK Kineto Box hits with pIC50

PI: Pilar Manzano
Published: 6/16/2016
GSK Kineto Box Project (TCAKS) 592
Using whole-cell phenotypic assays, the GlaxoSmithKline high-throughput screening (HTS) diversity set of 1.8 million compounds was screened against the three kinetoplastids most relevant to human disease, i.e. Leishmania donovani, Trypanosoma cruzi and Trypanosoma brucei. Secondary confirmatory and orthogonal intracellular anti-parasiticidal assays were conducted, and the potential for non-specific cytotoxicity determined. Hit compounds were chemically clustered and triaged for desirable physicochemical properties. The hypothetical biological target space covered by these diversity sets was investigated through bioinformatics methodologies. Consequently, three anti-kinetoplastid chemical boxes of approximately 200 compounds each were assembled. This data-set includes hit compounds and all associated screening results.


PI: Mark Parisi
Published: 3/3/2016
ASINEX has been working on the design and synthesis of protein-protein interaction (PPI) libraries since 2008. The latest generation of ASINEX PPI Library comprises molecules of various sizes, frameworks, and shapes ranging from fragment-like entities to macrocyclic derivatives designed as secondary structure mimetics or as epitope mimetics.

VENDOR: ASINEX Elite Library

PI: Mark Parisi
Published: 3/3/2016
ASINEX 12960
What issues are there after the initial “hit?” Asinex has addressed these issues with extensive ADME profiling, optimal design for easy medchem modification, and IP assessment to ensure novelty.

VENDOR: ASINEX Phenotypic Library

PI: Mark Parisi
Published: 3/3/2016
Asinex runs both targeted based and phenotypic assays in house and uses the experimental information it gathers to create both its target based and diverse screening sets. Through this experience, Asinex has created a phenotypic screening set; filters for this set are as follows:
MW:200-450, clogP:-1.0–7.0, clogD(pH 7.4):-5.0–4.0, Rot.Bond:0-10, HA:1-10, HD:1-5, TPSA:15-135 A, N+O:2-10, HAC:19-34, Dipole:0.3–3.30, SHP2:0.240–0.450.

VENDOR: ASINEX Diversity Library

PI: Mark Parisi
Published: 3/3/2016
Diversity continues to be a powerful screening tool, especially at the early “probe” stage of drug discovery. In creating this set, Asinex has applied computational tools to ensure chemical space is properly represented while also incorporating elements of its “Elite” and “BioDesign” concepts.


PI: Mark Parisi
Published: 3/3/2016
ASINEX’s BioDesign approach incorporates key structural features of known pharmacologically relevant natural products (e.g. alkaloids and other secondary metabolites) into synthetically feasible medicinal chemistry scaffolds.

CATALOG: Distributed Drug Discovery (D3) – IUPUI

PI: M. J. O’Donnell and W. L. Scott
Published: 2/24/2016
IUPUI – D3 Enum 73K N-AcylAA-OH, -OMe, -NH2 73234
A free, open-access virtual catalog/library of >73,000 molecules: (a) N-Acyl Unnatural α-Amino Acids, (b) Methyl Esters of N-Acyl Unnatural α-Amino Acids, and (c) Primary Amides of N-Acyl Unnatural α-Amino Acids. The molecules in the catalog were obtained by an enumeration based on the solid-phase combinatorial alkylation of a glycine anion equivalent with 100 R1X followed by N-acylation with 100 R2CO2H and resin cleavage (TFA, MeOH/Et3N, or TFA, respectively). The legacy data set of 48,818 molecules (above a and b sets plus R1X and R2CO2H inputs) was published on 1/1/2009. We encourage colleagues to communicate with us concerning interest in the D3 project (E-mail: [email protected]<mailto:[email protected]> or [email protected]<mailto:[email protected]>). References: J. Comb. Chem. 2009, 11, 3-13, 14-33, 34-43; J. Org. Chem. 2014, 79, 3140-51; J. Chem. Educ. 2015, 92, 819-26.

MALARIA: Biochemical screen of 5 P. falciparum kinases vs. GSK’s TCAMS

PI: Gregory J. Crowther
Published: 2/3/2016
Gregory J. Crowther 13451
~13,500 cell-active compounds were screened for activity against five different protein kinases. GlaxoSmithKline’s Tres Cantos Antimalarial Set (TCAMS) was screened in biochemical assays of Plasmodium falciparum calcium-dependent protein kinases 1 and 4 (CDPK1/PF3D7_0217500 and CDPK4/PF3D7_0717500), mitogen-associated protein kinase 2 (MAPK2/MAP2/PF3D7_1113900), protein kinase 6 (PK6/PF3D7_1337100), and protein kinase 7 (PK7/PF3D7_0213400). Novel potent inhibitors (IC50 < 1 µM) were discovered for three of the kinases: CDPK1, CDPK4, and PK6. The PK6 inhibitors are the most potent yet discovered for this enzyme and deserve further scrutiny.

Public Dark Matter Compounds

PI: Guillermo Morales
Published: 12/7/2015
Dark Matter Compounds 139352
Novartis found that 803,990 of their compounds had been tested in at least Novartis 100 assays and 112,872 compounds were inactive (14.0%). And an analysis of NIH data showed that 363,598 compounds had been tested in at least 100 assays where 131,726 compounds were inactive (36.2%).
Anne Mai Wassermann, Eugen Lounkine, Dominic Hoepfner, Gaelle Le Goff, Frederick J King, Christian Studer, John M Peltier, Melissa L Grippo, Vivian Prindle, Jianshi Tao, Ansgar Schuffenhauer, Iain M Wallace, Shanni Chen, Philipp Krastel, Amanda Cobos-Correa, Christian N Parker, John W Davies & Meir Glick. Dark chemical matter as a promising starting point for drug lead discovery. Nature Chemical Biology 2015, Vol. 11, pp. 958–966 (doi: 10.1038/nchembio.1936)

ADME: AZ Public ChEMBL Data

PI: Sean Ekins
Published: 10/5/2015
AZ Public ChEMBL Data 5799
Experimental in vitro DMPK and physicochemical data on a set of publicly disclosed compounds determined at AstraZeneca. The references provided for the assays exemplify the experimental procedures used in generating the data.

% bound to plasma by equilibrium dialysis. Compound is incubated with whole guinea pig plasma at 37C for >5hrs. Method described in B. Testa et al (Eds.), Pharmacokinetic Profiling in Drug Research: Biological, Physicochemical, and Computational Strategies, Wiley-VCH, Weinheim, 2006, pp.119-141. Experimental range 10% to 99.95% bound.

% bound to plasma by equilibrium dialysis. Compound is incubated with whole dog plasma at 37C for >5hrs. Method described in B. Testa et al (Eds.), Pharmacokinetic Profiling in Drug Research: Biological, Physicochemical, and Computational Strategies, Wiley-VCH, Weinheim, 2006, pp.119-141. Experimental range 10% to 99.95% bound.

% bound to plasma by equilibrium dialysis. Compound is incubated with whole rat plasma at 37C for >5hrs. Method described in B. Testa et al (Eds.), Pharmacokinetic Profiling in Drug Research: Biological, Physicochemical, and Computational Strategies, Wiley-VCH, Weinheim, 2006, pp.119-141. Experimental range 10% to 99.95% bound.

% bound to plasma by equilibrium dialysis. Compound is incubated with whole mouse plasma at 37C for >5hrs. Method described in B. Testa et al (Eds.), Pharmacokinetic Profiling in Drug Research: Biological, Physicochemical, and Computational Strategies, Wiley-VCH, Weinheim, 2006, pp.119-141. Experimental range 10% to 99.95% bound.

Intrinsic clearance measured in human hepatocytes following incubation at 37C. Experimental range <3 to >150 microL/min/1E6 cells. Rapid Commun. Mass Spectrom. 2010, 24, 1730-1736.

Most basic pKa value (pKa B1) determined by absorption and potentiometric titration using standard methodology from Sirius Analytical. Experimental range Bases: >= 2.

Second most acidic pKa value (pKa A2) determined by absorption and potentiometric titration using standard methodology from Sirius Analytical. Experimental range Acids: <= 11.

Third most basic pKa value (pKa B3) determined by absorption and potentiometric titration using standard methodology from Sirius Analytical. Experimental range Bases: >= 2.

Second most basic pKa value (pKa B2) determined by absorption and potentiometric titration using standard methodology from Sirius Analytical. Experimental range Bases: >= 2.

Most acidic pKa value (pKa A1) determined by absorption and potentiometric titration using standard methodology from Sirius Analytical. Experimental range Acids: <= 11.

PDB Ligands

PI: Dale R. Cameron, Ph.D., M.C.I.C., P.Chem.
Published: 8/3/2015
Protein Data Bank (PDB) 16826
Ligand information is extracted from the PDB, filtered to remove “polymer” and other related “non-free” ligands as well as metals or metal binding ligands. Updates to the filtering procedure may occur without warning. Data is provided as is with no additional curation or error correction. Links to PDB are provided by the RCSB PBD and can be cited as

H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne (2000) The Protein Data Bank Nucleic Acids Research, 28: 235-242.

Please report broken links, requests for additional data, etc. to the vault administrator

EBOLA: Small molecule inhibitors of Ebola virus

PI: Dr. Nadia Litterman
Published: 2/2/2015
Nadia’s Sandbox 55
This shared dataset contains 55 small molecules from the literature (up to Jan 2015) which have in vitro and or in vivo activity against the Ebola virus and various disease models. We have included an evaluation from an experienced medicinal chemist as well as results of PAINS filtering. (This work has been submitted for publication by Nadia Litterman, Christopher Lipinski and Sean Ekins to F1000Research).

VENDOR: Synthonix – Building Better Bonds

Published: 1/2/2015 10286
Synthonix helps medicinal chemists push the boundaries of drug discovery by providing a catalog of 10286 building blocks that allow them explore more challenging chemical space, and expand the range of potentially significant therapeutic targets to treat the world’s chronic and curable diseases. Synthonix, Inc : 919-875-9277; General E-mail: [email protected]; Synthonix Ltd (Europe Office): Office: +44 1223 597934; E-mail: [email protected]

PROBES: NIH Chemical Probes

PI: Christopher Lipinski
Published: 11/12/2014
Probes Vault 319
The National Institutes of Health (NIH) has funded extensive HTS efforts, estimated more than $576 million, in both intra-mural and academic centers to identify small molecule chemical probes or tool compounds via the Molecular Libraries Screening Center Network (MLSCN) and the Molecular Library Probe Production Center Network (MLPCN). For compounds to be elected as probes, various definitions, based on a combination of potency, selectivity, solubility, and availability, have been used. To date the NIH-funded academic screening centers have discovered more than 300 chemical probes. This collection includes probe structures, targets, anti-targets, IC50 values, and other references. It also includes a variety of measures of drug-likeness including the desirability score as assigned by Dr. Chris Lipinski as described in “Computational Prediction and Validation of an Expert’s Evaluation of Chemical Probes.” Litterman NK, Lipinski CA, Bunin BA, Ekins S. J Chem Inf Model. (2014)

VENDOR: Azepine Ltd. Building Blocks Collection

PI: Julia
Published: 10/8/2014
Azepine Ltd. 600
600 building blocks, IN STOCK at competitive prices. Contact [email protected]

NEU-CSIC-GSK Kinase-Targeted HTS

PI: Michael Pollastri
Published: 9/25/2014
Pollastri Lab – Northeastern University 78
This data set contains the published results of a high-throughput screen performed via collaboration between Northeastern University (Pollastri Laboratory), the CSIC (Navarro Laboratory), and GlaxoSmithKline Tres Cantos Laboratory (Diseases of the Developing World DPU). The article is Diaz et al, PLoS-NTDs:

DOI: 10.1371/journal.pntd.0003253

Please contact [email protected] with questions

VENDOR: Vitas-M Laboratory Stock HTS Collection

Published: 7/11/2014
Vitas-M Laboratory 388375
Vitas-M Laboratory, LTD. Collection of HTS compounds is about 400 000 individual molecules, in stock. All of them are available for quick delivery in different formats including mg, micromole, dry powder, DMSO solution, and dry film. Irina Ryabushenko: [email protected]

VENDOR: Vitas-M Laboratory Building Blocks

Published: 7/10/2014
Vitas-M Laboratory 33297
Vitas-M Laboratory, LTD. Collection of organic building blocks contains more than 33 000 identified and tested items. Irina Ryabushenko: [email protected]

VENDOR: Vitas-M Laboratory Scaffolds

Published: 7/8/2014
Vitas-M Laboratory 2898
Vitas-M Laboratory, LTD. Collection of Scaffolds (Azalea project). Advanced ideas to synthesize drug-like mini-libraries. It is the best choice to acquire absolutely novel compounds that no other vendor offers. Irina Ryabushenko: [email protected]

VENDOR: Vitas-M Laboratory Fragments

Published: 7/8/2014
Vitas-M Laboratory 18631
Vitas-M Laboratory, LTD. Collection of Fragments (chemical substances passed through “Rule of 3” and other special filters) for Fragments Based Drug Discovery. Irina Ryabushenko: [email protected]

VENDOR: Life Chemicals- GPCR library

PI: Alexandr Kucherak
Published: 6/20/2014
Life Chemicals 15948
Similarity/pharmacophore search was based on Topomer Search prediction provided by Sybyl-X. First step – a similarity search assumed a comparison of entire stock compounds to known inhibitors derived from BindingeDB and ChemblDB. Second step – generation of 3D structures of known inhibitors and their co-alignment. This chemical spatial space was used as a template for fitting of the rest of “similar” compounds. However this is method was designed for “cherry-picking” and an alternative library can be done with virtual screening methods (all screening models a ready and proved with training sets) against such receptors – adenosine, chemokine, dopamine, gaba-, histamine, muscarinic, opioid, sphingosine.

VENDOR: Life Chemicals- Kinase by Similarity

PI: Alexandr Kucherak
Published: 6/20/2014
Life Chemicals 62467
Similarity search using MDL public keys and the Tanimoto similarity cut-off of 90%. Almost 25K reference compounds that tested active in 168 biological assays (more than 100 different kinase targets), were used for similarity search. All this compounds could be screened against more specific target up to the customer order.

VENDOR: Life Chemicals- Kinase by docking

PI: Alexandr Kucherak
Published: 6/20/2014
Life Chemicals 15174
Kinase library was prepared basing on virtual docking in a Sybyl environment. For this purpose a set of kinase structures’ binding sites (about 20) were aligned and analyzed. Such superposed sites were used for structure-based pharmacophore modelling via Unity module from Sybyl-X. After all preparation an entire 3D stock was screened against this multi-pharmacophore model and in the end a top-ranking was performed.

VENDOR: Life Chemicals- Nuclear Receptors

PI: Alexandr Kucherak
Published: 6/20/2014
Life Chemicals 9896
Life Chemicals. Virtual docking and similarity/pharmacophore search.

VENDOR: Life Chemicals- CNS Library

PI: Alexandr Kucherak
Published: 6/20/2014
Life Chemicals 16535
CNS filters which are described in the literature were used as a sieve for our entire stock. As it was shown the only compounds with such parameters can have appropriate characteristics for nervous tissue permeability. All descriptors were obtained from Spreadsheets and Volsurf modules of Sybyl. (MW 200 = 350 cLogP =< 3.6 H-Bond Acceptors =< 8 H-Bond Donors =< 5 tPSA =< 120 Rotatable Bonds =< 5 LogBB1 = -3.0 to 1.0)

VENDOR: Life Chemicals- Natural Product-like Library

PI: Alexandr Kucherak
Published: 6/20/2014
Life Chemicals 7808
First method was based on statistical anlysis of descriptors. Previously a large database of NPs was analyzed to study NP scaffolds by arranging them in the form of a tree. Thus analysis of property distribution of more than 130 000 NP structures as well as identification of substructures typical for particular classes of natural compounds were carried out to generate a set of fragments usually present in natural compounds. This method was tested on CRC Dictionary of Natural Products (DNP) and synthetic molecules (SMs). Another method is based on scaffold similarity assessment. The number of atom signatures (from fragmnets) generated for a molecule is equal to the number of atoms that make up the molecule. Every atom signature independently represent a structural feature/fragment of the molecule, and an individual score for it is calculated. higher number of atoms from gaining higher score. To reproduce such experiment we used an implemented module Chemistry Development Kit in CDK-Taverna 2.0. It contains a NP-Likeness scorer v1.4.1 which calculates Natural Product(NP)-likeness of a molecule, i.e. the similarity of the molecule to the structure space covered by known natural products. All results were scored and ranged from -3 to +3.

VENDOR: Life Chemicals- Screening collection

PI: Alexandr Kucherak
Published: 6/20/2014
Life Chemicals 371998
Carefully designed, novel, drug-like small molecules with Lipinski rule of 5 and the only reason for deviation from the set of this parameters is a unique scaffold or non-standard chemistry. It is ready for application of medicinal chemistry filters like PAIN or any target-focused filters (solubility, permeability, BBB).

VENDOR: Life Chemicals- Fragments with Guaranteed Solubility

PI: Alexandr Kucherak
Published: 6/20/2014
Life Chemicals 8241
Fragment compounds were selected by filtering of entire LC-stock with modified “Rule of three”. Fragments have been tested for solubility in analytical laboratory. Solubility is guaranteed at 200mM concentration in DMSO, and 75% of fragments are soluble in pH7.5 buffer at 1mM concentration.

TB: In vivo mouse efficacy from literature

PI: Sean Ekins, PhD
Published: 4/10/2014
TB in-vivo data2 778
Looking Back To The Future: Predicting In vivo Efficacy of Small Molecules Versus Mycobacterium tuberculosis. Selecting and translating in vitro leads for a disease into molecules with in vivo activity in an animal model of the disease is a challenge that takes considerable time and money. We demonstrate learning from in vivo active and inactive compounds using machine learning classification models (Bayesian, Support Vector Machines and recursive partitioning) consisting of 773 compounds. The Bayesian model predicted 8 out of 11 additional in vivo actives not included in the model as an external test set. Curation of seventy years of Mtb data can therefore provide statistically robust computational models to focus resources on in vivo active small molecule antituberculars. This highlights a cost effective predictor for in vivo testing elsewhere in other diseases. PMID:24665947

TB: Data for TB Mobile 2

PI: Sean Ekins
Published: 3/19/2014
TB Mobile 2.0 Updates 79
79 compounds selected from recent papers with one or more target in TB added to TB Mobile for version 2 of the app. 20 additional molecules were used as a test set. The paper is submitted.

PARASITE: MMV malaria box screen of Schistosoma mansoni

Published: 11/6/2013
CDIPD Vault 400
Whole-organism screens of Schistosoma mansoni somules (post-infective larvae) and adults with the 400 compounds that comprise the MMV Malaria Box ( Only those Malaria box ‘Drug-like’ compounds yielding the most severe phenotypes vs. somules were tested against adults. The data are also uploaded to ChEMBL. Contact Conor Caffrey, Center for Discovery and Innovation in Parasitic Diseases (, UCSF ([email protected]).

Kinase: Kinase Catalytic Activity (Theonie Anastassiadis Publication in Nature Biotechnology)

PI: Theonie Anastassiadis
Published: 8/30/2013
Kinase Catalytic Activity 178
Kinase Catalytic Activity
Nature Biotechnology 2011 October 30; 29(11): 1039–1045.

The library tested comprised 178 compounds known to inhibit kinases from all major protein kinase subfamilies

For simplicity, all compounds were tested at a concentration of 0.5 µM in the presence of 10 µM ATP. 0.5 µM was chosen despite an average reported IC50 for these compounds toward their primary targets of 66 nM in order to capture weaker off-target inhibitory activity.

Each kinase-inhibitor pair was tested in duplicate and results were expressed as average substrate phosphorylation as a percentage of solvent control reactions (henceforth referred to as “remaining kinase activity”).

Mean remaining kinase activity for each kinase-inhibitor pair is presented. Kinase activity data was expressed as the percent remaining kinase activity in test samples compared to vehicle (dimethyl sulfoxide) reactions.

TB: Update drugs and leads with targets

Published: 6/14/2013
TB: drugs and leads with targets – update 38
Published compounds from the recent literature for TB with known targets to be used as an update also for the TB Mobile App

KINASE: GSK Published Kinase Inhibitor Set (PKIS)

Published: 6/6/2013
Kinome2 364
The GSK Published Kinase Inhibitor Set (PKIS) is a set of 367 protein kinase inhibitors, which has been annotated for protein kinase family activity and is available for public screening efforts. Detailed information on the screening set can be found at the links shown below. The ChEMBL database has been the “go-to” site for bioassay data on this set. In the spirit of improving access to important data, we have gathered the PKIS data that ChEMBL has kindly made available, and processed it so it could be accessed here at the Collaborative Drug Discovery (CDD) site (much like we have done previously for the Kinase SARfari database).

The transfer to CDD makes the data available in a more “med-chemist” friendly manner. We also did some tidying up of the data set. For example there are actually only 364 compounds (some duplicates were due to salt forms or alternate names of the same molecule). We also tried to normalize target names where possible (for example, the kinases IKKA, IKKB and IKKE were called IKK-alpha, IKK-beta, IKK-epsilon for the dataset from UNC). Not that we’re perfect… we appreciate any corrections to our dataset as well!

To summarize, there are 364 compounds that have been tested against 225 targets at 0.1 and 1 uM. In this dataset, there is only one protocol, but the 225 targets are listed in one readout. Concentration is also a readout, so it is easy to limit searches to screens run at 1 and/or 0.1 uM.

1) More information on the GSK PKIS

2) Previous ChEMBL kinase data on CDD

KINASE: ChEMBL Kinase SARfari Compounds & BioAssay Data

Published: 3/27/2013
CDD Vault 54211
A valuable resource available at ChEMBL is the Kinase SARfari, “an integrated chemogenomics workbench focused on kinases. The system incorporates and links kinase sequence, structure, compounds and screening data”. A highly useful resource, this database makes available a large amount of SAR data for the kinase active compounds against a wide range of kinases in a broad array of assays, much of it manually mined and curated from the literature. To make this data available in the CDD interface, we took the core table of Kinase SARfari and merged it with another key table from the ChEMBL database, providing a field describing the assay utilized in each record in much greater detail than is available in native SARfari. We have now made this merged dataset available via the CDD interface. Detailed in vitro data is avaiable for 400 kinases. In addition, in vivo functional, as well as ADMET data is posted as well.


PI: Bob Reynolds
Published: 3/15/2013
TB ARRA 1924
Data from SRI (Bob Reynolds) and Scott Franzblau group – paper submitted by Ekins et al.
Hits from previous SRI screens were used to look for similar compounds in vendor libraries, clustered and tested in vitro in a series of accepted panels of screens for new drug discovery candidates. The compounds were also used as a test set for previously generated Bayesian models built with bioactivity and cytotoxicity information.


PI: Sean Ekins, PhD
Published: 2/8/2013
TB GSK 177
Supplemental data from the Ballell et al paper ChemMedChem 2013 in press “fueling open-source drug discovery: 177 small-molecule leads against tuberculosis”
Original datasets are hosted at only M.tb data is shown here but more BCG data is available at ChEMBL

TRYPANOSOME: Chagas Disease Literature Compounds

Published: 12/21/2012
Chagas Public Data 531
Compound structures and literature references were curated for 531 molecules tested against Trypanosoma cruzi in vitro or in vivo in the published literature.

TRYPANOSOME: Optimization of specific chemical series against human African Trypanosomiasis (HAT)

Published: 12/12/2012
Chagas Public Data 5559
SCYNEXIS Inc, as a member of the DNDi HAT Lead Optimization Consortium developed and screened 4926 compounds for activity against T. brucei. Compound structures and in vitro activity data against T. brucei brucei are included. Cytotoxicity data and activity against the related eukaryotic parasites T. brucei rhodesiense, L. donavani, and P. falciparum for a subset of 34 compounds. All of the reported compound series are no longer in development for HAT as they were found to have poor selectivity or properties incompatible with in vivo activity.

TRYPANOSOME: DNDi-Optimization of fenarimol series for treatment of Chagas disease

Published: 12/9/2012
Chagas Public Data 743
The DNDi Lead Optimization Consortium, including Epichem, Murdoch University, and CDCO, developed and screened an SAR series based on the plant fungicide fenarimol. DNDi made public compound structures, T. cruzi activity data, and L-6 cell toxicity data for 743 compounds from this series in ChEMBL-NTD. Compounds and biological assay data are included here in CDD Public.

TRYPANOSOME: Broad Primary HTS to Identify Inhibitors of T.Cruzi Replication

Published: 12/6/2012
Chagas Public Data 303230
The Broad Institute performed a high-throughput screen of 303,224 compounds in duplicate in the recombinant Tulahuen strain of Trypanosoma cruzi stably expressing beta-galactosidase reporter co-cultured with host cell, mouse fibroblast NIH3T3. Of the 4,394 hits, 4,063 were further evaluated for inhibitory activity and host cell toxicity. Finally, 27 compounds were selected as potential probe compounds and further validated. Data from the primary screen and subsequent secondary assays were deposited PubChem. Chemical compounds and biological assay data for the primary screen and six secondary assays from PubChem are included here in CDD Public.

TB: Guzman et al., M.tb. MurE ligase inhibitors

PI: Sean Ekins
Published: 12/6/2012
CDD – Sean Ekins 8
Whole cell and target based screening data from the following TB publication: Guzman JD, Gupta A, Evangelopoulos D, Basavannacharya C, Pabon LC, Plazas EA, Muñoz DR, Delgado WA, Cuca LE, Ribon W, Gibbons S, Bhakta S. J Antimicrob Chemother. 2010 Oct;65(10):2101-7. Anti-tubercular screening of natural products from Colombian plants: 3-methoxynordomesticine, an inhibitor of MurE ligase of Mycobacterium tuberculosis.

VENDOR: NIH Clinical Collection 2 array (281 molecules)

PI: Project Manager: Mei Steele
Published: 11/21/2012
NIH Clinical Collections 281
The NIH Clinical Collection 2 are plated arrays 281 small molecules that have a history of use in human clinical trials. The collection was assembled by the National Institutes of Health (NIH) through the Molecular Libraries Roadmap Initiative as part of its mission to enable the use of compound screens in biomedical research.

VENDOR: NIH Clinical Collection array (446 molecules)

PI: Project Manager: Mei Steele
Published: 11/21/2012
NIH Clinical Collections 446
The NIH Clinical Collection is plated array of 446 small molecules that have a history of use in human clinical trials. The collection was assembled by the National Institutes of Health (NIH) through the Molecular Libraries Roadmap Initiative as part of its mission to enable the use of compound screens in biomedical research.

TB: Drugs and leads with targets – data used in mobile app

Published: 10/23/2012
SRI molecules and targets for mobile app 707
Updated Data curated for TB targets with in vivo essentiality
information from TBDB, Biocyc, Metacyc, PDB and Pubmed as well as
other references by Malabika Sarker at Stanford Research Institute.
Gyanu Lamichhane at Johns Hopkins University provided essentiality

Explore this dataset on mobile:

TOX: Drugs and chemicals classified by hepatotoxicity

Published: 7/16/2012
CDD Vault 83072
A list of drugs and chemicals with a classification scheme based on clinical data for hepatotoxicity has been assembled by Pfizer (Hu 2008) previously in order to evaluate an in vitro human hepatocyte imaging assay technology (HIAT), resulting in a concordance of 75% with clinical hepatotoxicity. This same dataset of compounds that do or do not cause drug induced Liver injury (DILI) has been used along with molecular descriptors for in silico prediction via Bayesian models.

TB: SRI Molecules with Whole-Cell Activity Against TB

PI: Sean Ekins, PhD
Published: 4/24/2012
SRI Group Vault 23
Molecules evaluated in Pharm Res. 2012 Apr 4. PMID: 22477069

Combining Cheminformatics Methods and Pathway Analysis to Identify Molecules with Whole-Cell Activity Against Mycobacterium Tuberculosis.

Sarker M, Talcott C, Madrid P, Chopra S, Bunin BA, Lamichhane G, Freundlich JS, Ekins S.

MALARIA: MMV Malaria Box

Published: 3/29/2012
Public: Malaria Box 400
Molecules from MMV Malaria Box, ChEMBL-NTD ( : MMV Malaria Box, Simon Macdonald, Paul Willis, Paul Kowalczyk, Thomas Spangenberg, Jeremy Burrows and Tim Wells. Medicines for Malaria Venture (MMV), PO Box 1826, 20, rte de Pré-Bois, 1215 Geneva 15, Switzerland and SCYNEXIS Inc. P.O. Box 12878 Research Triangle Park, North Carolina 27709-2878 USA.

All compounds in the Malaria Box have been screened in vitro against 3D7 (chloroquine (CQ) sensitive but sulfadoxine resistant strain of P. falciparum) and cytotoxicity assays were performed on human embryonic kidney cell lines (HEK-293). Data are expressed as EC50 in nM for the falciparum data.

ADME: – A Commercial Repository of High Quality ADME Data

PI: George Grass
Published: 1/13/2012
G2 Research 1760
Examples of: Caco-2 Permeability, Equilibrium Solubility @ 5pH Values, Protein Binding Human, Protein Binding Rat, Rabbit Intestinal Permeability, Human Blood Plasma Partitioning & Hematocrit. For full data sets and models, directly contact George Glass, Pharm.D. Ph.D at [email protected] (distributed via CDD)

VENDOR: Porse Building Blocks Collection

Published: 1/13/2012
CDD Vault 29241
Porse File Chemical Co. is devoted to custom novel compound synthesis for drug discovery, and provides a wide product range with competitive prices and good quality. The current set is a selected subset of 1554 new diverse compounds and building blocks in the Morpholine, Piperidine, Piperazine, Pyrimidine, amino acid and API families., [email protected] +86-20-28069055

PARASITES: Schistosoma mansoni schistosomula: Microsource Spectrum & Killer Collections

Published: 10/5/2011
Brian Suzuki’s Sandbox 119
Schistosoma mansoni schistosomula: Phenotypic Screen of the Microsource Spectrum & Killer Collections.

PI: Conor R. Caffrey

Published: 10/5/2011

CDD: Public Data 119 hits

As part of a drug re-purposing (re-positioning) strategy to identify novel anti-parasitics at the UCSF Sandler Center for Drug Discovery, we developed a partially automated whole organism (phenotypic) screen for the bloodfluke that causes the infectious tropical disease, schistosomiasis. We screened the 1,260 compounds of the above-stated collections that include drugs, drug-like compounds, natural products and miscellaneous compounds. We report the phenotypic alterations in larval stages (schistosomula) of Schistosoma mansoni using simple descriptors to convey the multiple and dynamic responses of the parasite to compound insult. Full quantification of the phenotypic responses is ongoing. The data presented pertain to only the ‘hit’ compounds; the full listing of compounds in the respective collections can be obtained from Microsource Discovery Systems Inc. Contact [email protected] for more details. Drug discovery for schistosomiasis: hit and lead compounds identified in a library of known drugs by medium-throughput phenotypic screening. Abdulla MH, Ruelas DS, Wolff B, Snedecor J, Lim KC, Xu F, Renslo AR, Williams J, McKerrow JH, Caffrey CR. PLoS Negl Trop Dis. 2009 Jul 14;3(7):e478.PMID: 19597541

TB: SRI Kinase Library Phenotypic Screen

Published: 8/29/2011
CDD Vault 23823
Kinase targets are being pursued in a variety of diseases beyond
cancer, including immune and metabolic as well as viral, parasitic,
fungal and bacterial. In particular, there is a relatively recent
interest in kinase and ATP-binding targets in Mycobacterium
tuberculosis in order to identify inhibitors and potential drugs for
essential proteins that are not targeted by current drug regimens.
Herein, we report the high throughput screening results for a targeted
library of approximately 26,000 compounds that was designed based on current kinase inhibitor scaffolds and known kinase binding sites. The phenotypic data presented herein may form the basis for selecting scaffolds/compounds for further enzymatic screens against specific kinase or other ATP-binding targets in Mycobacterium tuberculosis based on the apparent activity against the whole bacteria in vitro.

PMID: 21708485
Tuberculosis (Edinb). 2011 Jun 25. [Epub ahead of print]
Copyright © 2011 Elsevier Ltd. All rights reserved.
Contact Melinda Sosa for more details: [email protected]
High throughput screening of a library based on kinase inhibitor
scaffolds against Mycobacterium tuberculosis H37Rv.
Reynolds RC, Ananthan S, Faaleolea E, Hobrath JV, Kwong CD, Maddox C, Rasmussen L, Sosa MI, Thammasuvimol E, White EL, Zhang W, Secrist JA 3rd.
Source: Southern Research Institute, 2000 Ninth Avenue South,
Birmingham, AL 35205, USA.

FDA APPROVED: NCGC Pharmaceutical Collection (NPC) V1.1.0

PI: Noel Southall
Published: 8/8/2011
NCGC Pharmaceutical Collection NPC V1.1.0 14579
The NCGC Pharmaceutical Collection: A Comprehensive Resource of Clinically Approved Drugs Enabling Repurposing and Chemical Genomics. Huang, R., Southall, N., Wang, Y., Yasgar, A., Shinn, P., Jadhav, A., Nguyen, D., Austin, C. Sci Transl Med 27 April 2011: Vol. 3, Issue 80, p. 80ps16.

VENDOR: BioBlocks Catalog with Pricing Information

PI: Doug Murphy
Published: 8/3/2011
BioBlocks 2971
2989 compounds.

BioBlocks offers a focused collection of over 2200 scaffolds, building blocks and fragments which are pre-qualified as drug components. The majority of these compounds are uniquely offered by BioBlocks and have found applications ranging from intermediates for drug discovery to surrogate amino acids in peptide chemistry.

Up-to-date details about BioBlocks building blocks are available at

TOX: Drug induced liver injury data (DILI)

Published: 4/29/2011
BBB 519
Drug induced liver injury data – training set is experimental data from Jim Xu and test set represents literature data.
published in Drug Metab Dispos. 2010 Dec;38(12):2302-8. Epub 2010 Sep 15. A predictive ligand-based Bayesian model for human drug-induced liver injury.
Ekins S, Williams AJ, Xu JJ.

TB: Target database for In vivo essential genes

PI: Sean Ekins
Published: 4/21/2011
SRI TB Target Database 314
Data curated for TB targets with in vivo essentiality information from TBDB, Biocyc, Metacyc, PDB and Pubmed as well as other references collated by Dr. Malabika Sarker at Stanford Research Institute. Dr. Gyanu Lamichhane at Johns Hopkins University is kindly acknowledged for providing essentiality information.
**please note there are no small molecules associated with this dataset**

VENDOR: Enamine Representative Diverse Screening Library

PI: Dmytro Mykytenko
Published: 4/12/2011
Enamine 200000
Original 200K diverse screening library was generated especially for Collaborative Drug
Discovery users from the world’s largest stock of commercially available screening compounds
(over 1.7 M species). The library features exclusive drug-like compounds with refined ADME
properties. Our high quality compounds can be cherry-picked and supplied immediately in
different formats.

REPOSITIONING, FDA APPROVED: Drugs Repurposed using HTS methods

Published: 3/18/2011
In vitro repurposing 109
Drugs identified with new uses using HTS methods. This table greatly extends a previously published version “Ekins S, Williams AJ, Krasowski MD, Freundlich JS. In silico repositioning of approved drugs for rare and neglected diseases Drug Discov Today. 2011 Mar 1. PMID: 21376136 doi:10.1016/j.drudis.2011.02.016 The table lists molecules, Old use / target, new use/ target, how discovered and references.

Abbreviations: CCR5, Chemokine receptor 5; DHFR, Dihydrofolate reductase; DOA, Drugs of abuse, FDA, Food and Drug Administration; GLT1, Glutamate transporter 1; HSP-90, Heat shock protein 90; JHCCL, John Hopkins Clinical Compound Library; Mtb, Mycobacterium tuberculosis; NK-1, neurokinin- 1 receptor; OCTN2.

REPOSITIONING, FDA APPROVED: Orphan-designated products

Published: 3/18/2011
Rare disease repurposing 76
FDA Table 2 – from the FDA resource, the rare disease research database (RDRD), which lists Orphan-designated products ( with at least one marketing approval for a rare disease indication. This data was analyzed by Ekins and Williams (paper submitted).

REPOSITIONING, FDA APPROVED: Orphan-designated products

Published: 3/18/2011
Rare disease repurposing 105
FDA Table 1 – from the FDA resource, the rare disease research database (RDRD), which lists Orphan-designated products ( with at least one marketing approval for a common disease indication.
The FDA did not associate the data with molecule structures.

VENDOR: Colorado Center for Drug Discovery Pilot Library

PI: Greg Miknis, Associate Director
Published: 3/7/2011
C2D2 Public 2240
The library contains structurally diverse small molecules which conform to drug like criteria. Several chemotypes are represented and the library is designed to be applicable to a wide variety of potential targets.

To request information about the collection, please send a request to [email protected]

LIPID: Lipid Maps Structure Database

PI: Lipidomics Gateway
Published: 2/11/2011
Lipid Maps Database 22215
The Lipid Maps ( structures were annotated with 5 common ions (H+,2H++, K+, Na+, NH4+) including mammalian fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterol lipids, and prenol lipids. The structures and ions are searchable by structure and MW to facilitate identification of novel lipids.

TB: Mycobacterium drugome

Published: 11/5/2010
virtual metabolites 274
Dataset of 274 drugs (approved for human use in US and Europe) from a publication by Kinnings et al., PLoS Computational Biology vol 6: e1000976 (2010)
Drugs co-crystallized with at least one structure in PDB.

This dataset can be used with the other TB screening datasets in CDD to determine which of these approved drugs have activity against Mtb (from the literature.

TB: Inhibitors of non-replicating Mtb from the literature

PI: Sean Ekins
Published: 10/28/2010
CDD – Sean Ekins 26
Structures and data from published papers:
Darby and Nathan J Antimicrob Chemother 2010: 65: 1424-1427
Bryk et al., Cell Host and Microbe 2008: 3: 137-145
Lin et al., Arch Biochem Biophys. 2010 501: 214-220
Lin et al., J Biol Chem 2008: 283: 34423-34431
de Cavalho et al: J Med Chem 2009: 52: 5789-5792
Lin et al., Nature 2009: 461: 621-626

VENDOR: Astatech, Inc. Building Block Collection

Published: 10/15/2010
Astatech, Inc. 6140
AstaTech, Inc. offers advanced and novel intermediates to facilitate the drug discovery process. Our broad selection includes building blocks, novel amines, protected amines, unnatural amino acids, ketones, aldehydes, heterocycles, isatoic anhydrides, boroinc acids and chiral intermediates. Contact [email protected] for ordering information.

VENDOR: Chemik 2010 Catalogue

Published: 10/5/2010
CDD Vault 3889
Chemik has successfully assisted drug discovery companies like Wyeth on their early phase projects. We provide the raw material and key intermediates from grams to multi-tons for them. With 10-years of experience in this field, we can help our customers develop a new intermediate in 4-6 weeks with competitive pricing, great quality and continuous service.

MALARIA: Phenanthrene and Anthracene Aminoalcohols

Published: 9/21/2010
CDD Vault 35
Antimalarial data vs P. berghei in mice for halogen-substituted anthracene and phenanthrene N-di- and mono-alkylsubstituted aminoalcohol hydrochlorides. Twenty-seven compounds showed activity (Increase in Mean Survival Time >6 days); eight compounds were curative (IMST > 60 days). Table includes PubMed IDs for details and syntheses.

TB: BCG/MTB Activity

PI: Srinivasa Rao
Published: 9/15/2010
Novartis: TB Data 283
Aerobic BCG Activty (MIC50)- 274 compounds
Aerobic MTB Activity (MIC50)- 283 compounds
Anaerobic BCG ATP Activity (IC50)- 283 compounds
Anaerobic MTB ATP Activity (IC50)- 283 compounds
Cytotoxicity (CC50)- 223 compounds

keywords: Mycobacterium tuberculosis, Mycobacterium bovis, TB

MALARIA: JHU JHCCL Plasmodium falciparum inhibition

Published: 6/4/2010
Johns Hopkins – Sullivan (2008) 2693
Percent inhibition of 2663 approved drugs at 10 microM

TB, MALARIA: Bayesian predictions for GSK malaria hits

PI: Sean Ekins
Published: 5/28/2010
GSK Data Bayesian Models (Ekins, et al.) 13355
Predictions for the GSK malaria hits (published by Gamo et al., Nature 465: 305-310 (2010)) using the Bayesian models (published by Ekins et al., Mol BioSyst 6: 840-851 (2010)).
Cut offs for activity (220,000 model >0.31, 2,200 model > -1.37 are classed as actives in the whole cell screen).

MALARIA: St. Jude Children’s Research Hospital Whole Cell Malaria Dataset

PI: Kip Guy
Published: 5/26/2010
St. Jude – Malaria/Trypanosome Bioactives 1524
Supplemental data for Nature Article published by St. Jude CRH (Guiguemde, W, et al. Chemical genetics of Plasmodium falciparum. Nature 465, 311-315 (20 May 2010)), including 1524 structures tested in a primary screen, with additional data in eight protocols: Bland-Altman analysis, calculated ADMET properties, Phylochemogenetic screen, Sensitivity, Synergy, and Enzyme Assays, as well as a Thermal Melt Analysis.

MALARIA: Novartis GNF-Pf Dataset

Published: 5/21/2010
Novartis Malaria 5695
Plasmodium falciparum strains 3d7 (drug-susceptible) and W2 (chloroquine-, quinine-, pyrimethamine-, cycloguanil-, and sulfadoxine-resistant), obtained from MR4, were tested in an erythrocyte-based infection assay for susceptibility to inhibition of proliferation by selected compounds.

VENDOR: ASINEX Novel Anti-Malaria Screening Set

PI: Mark Parisi
Published: 5/20/2010
CONFIDENTIAL DATA SET: 594 Novel compounds from ASINEX. Please see the attached file which elaborates on ASINEX design.
FOR ACCESS: New CDD users- your registration will be passed through an approval process before access to the dataset is granted. Existing CDD users- please contact [email protected]

VENDOR: ASINEX Tres Cantos (GSK) Antimalarial Subset

PI: Mark Parisi
Published: 5/20/2010
278 ASINEX active anti Malaria data matching GSK data.

The corresponding dataset is proprietary and owned by ASINEX.

For more information, please contact Mark Parisi:

Email: [email protected]
Telephone: 1-877-ASINEX1
Fax: 1-336-721-1618

MALARIA: Tres Cantos Antimalarial Set (TCAMS)

PI: Javier Gamo
Published: 5/19/2010
GSK Anti-Malarial Data 13471
Screening of approximately 2 million compounds in GlaxoSmithKline’s screening library identified over 13,500 inhibitors of proliferation of P. falciparum in human erythrocytes. The work was carried out at Tres Cantos Medicine Development Campus, GlaxoSmithKline, Severa Ochoa 2, 28760 Tres Cantos, Spain.

TB: Sacchettini et. al. review – additional antituberculosis agents

Published: 2/5/2010
PK 18
Non-approved antituberculosis agents from Figure 1 in Sacchettini J.C., Rubin E.J. and Freundlich J.S. Drugs versus bugs: in pursuit of the persistent predator Mycobacterium tuberculosis, Nature Reviews Microbiology, 6, 41-52, (2008).

TB: Tuberculosis Small Molecule Patent Data

PI: Collaborative Drug Discovery
Published: 1/27/2010
TB Patent Data 20775
Structures and patent information regarding tuberculosis research from the US Patent and Trademark Office, European Patent Office, and World Intellectual Property Organization.

TB: Makarov et al., NM4TB consortia

PI: Sean Ekins
Published: 1/21/2010
CDD – Sean Ekins 32
Structure activity relationship data for 1,3-benzothiazin-4-ones (BTZ). Data obtained from the paper “Benzothiazinones Kill Mycobacterium tuberculosis by Blocking Arabinan Synthesis” published in Science by Makarov et al., 2009 and colleagues at the NM4TB consortia (PMID: 19299584).

VENDOR: TimTec Diversity Set

PI: Vendor
Published: 1/5/2010
TimTec 9998
Screening library of 10,000 diverse drug like compounds

VENDOR: TimTec OGT-Inhibitors Analogs SET

PI: Vendor
Published: 1/5/2010
TimTec 334
O-GlcNAc Transferase Inhibitors Analogs SET

VENDOR: TimTec ActiTarg-K, Kinase Modulators

PI: Vendor
Published: 1/5/2010
TimTec 6212
ActiTarg-K, counts over 6,000 compounds providing a high value screening library of drug-like molecules for identifying synthesis direction for new protein kinase inhibitors

VENDOR: TimTec Natural Product Derivatives Library

PI: Vendor
Published: 1/5/2010
TimTec 3001
NDL-3000 Natural Derivatives from TimTec

VENDOR: TimTec Natural Product Library

PI: Vendor
Published: 1/5/2010
TimTec 479
NPL Pure Natural Products from TimTec

VENDOR: Screening Library

Published: 10/26/2009
AsisChem 43121
A collection of over 40,000 drug-like, small molecule compounds available for your custom selection. All compounds are in stock up to 25mg.

VENDOR: Building Blocks

Published: 10/26/2009
AsisChem 176
A collection of compounds useful in drug discovery. All compounds if not in stock are available within a few weeks for amounts up to 10 grams.


PI: Robert Goldman
Published: 9/30/2009
Southern Research Institute 102634
Results of screening a commercial (ChemBridge) compound library for the ability to inhibit the growth of M. tuberculosis strain H37Rv. See PMID: 19758845

TB: EthR inhibitors (Willand et al.)

PI: Sean Ekins
Published: 9/28/2009
CDD – Sean Ekins 5
Drug-like inhibitors of the transcriptional repressor EthR. Molecules and data from Willand et al Nature Medicine 15: 537-544 (2009) PMID: 19412174

VENDOR, ADME: Benchmark Data from a Set of Structurally Diverse Commercial Drugs.

PI: Anders Karlen
Published: 6/11/2009
NM4TB: Karlen Group Site 24
A multivariate analysis of drugs on the Swedish market was the basis for the selection of a small, physicochemically diverse set of 24 drug compounds. Factors such as structural diversity, commercial availability, price, and a suitable analytical technique for quantification were considered in the selection. Lipophilicity, pKa, solubility, and permeability across human Caco-2 cell monolayers were measured for the compiled data set. We anticipate that this data set can serve as a benchmark set for validation of new experimental techniques or in silico models. It can also be used as a diverse starting data set for the development of new computational models.

Data taken from:
Presentation of a structurally diverse and commercially available drug data set for correlation and benchmarking studies.
Sköld C, Winiwarter S, Wernevik J, Bergström F, Engström L, Allen R, Box K, Comer J, Mole J, Hallberg A, Lennernäs H, Lundstedt T, Ungell AL, Karlén A.
J Med Chem. 2006 Nov 16;49(23):6660-71.

TB: Absorption Data from Published Literature

Published: 5/28/2009
CDD: TB Curated Literature 24
TB Absorption Data from reference article
Inhibition of siderophore biosynthesis by 2-triazole substituted analogues of 5′-O-[N-(salicyl)sulfamoyl]adenosine: antibacterial nucleosides effective against Mycobacterium tuberculosis.
Gupte, A.; Boshoff, H. I.; Wilson, D. J.; Neres, J.; Labello, N. P.; Somu, R. V.; Xing, C.; Barry, C. E.; Aldrich, C. C.
J Med Chem (2008) Vol 51, No 23, pp 7495-7507

Permeability data.

TB: Pharmacokinetic Data from Published Literature

Published: 5/28/2009
CDD: TB Curated Literature 28
TB Pharmacokinetic Data from Published Literature sources. SAR data for 28 unique, as well as common compounds.
Data includes PubMed citations, targets, cells and organisms tested, bioavailability, Vm, Vd, Cmax, etc.

TB: Toxicity Data from Published Literature

Published: 5/28/2009
CDD: TB Curated Literature 638
TB Toxicity Data from Published Literature sources. SAR data for 638 unique, as well as common compounds from PubMed references.
Data includes PubMed citations, targets, cells and organisms testes, cell viability, LD50, CC50, MNTD, etc.

TB: Efficacy Data from Published Literature

Published: 5/28/2009
CDD: TB Curated Literature 6768
TB Efficacy Data from Published Literature sources. SAR data for 6771 unique, as well as common compounds from over 300 PubMed references.
Data includes PubMed citations, targets, cells and organisms testes, MIC, % Inhibition, EC50-EC100, IC50, etc.


PI: Robert Goldman
Published: 5/8/2009
Southern Research Institute 214507
A diverse collection of over 200,000 compounds collected by the Molecular Libraries Small Molecule Repository (MLSMR) were made available to the Southern Research Molecular Libraries Screening Center in Spring 2008 for primary testing against Mtb H37Rv. The most active compounds from this primary screen were selected and tested at 10 concentrations in both a dose response assay against H37Rv as well as a cytotoxicity counterscreen using vero cells.

MALARIA: Johns Hopkins Clinical Compound Library

Published: 4/28/2009
Johns Hopkins – Sullivan (2008) 1878
Drugs were screened at a concentration of 10 μM. Synchronized ring stage parasites from chloroquine-sensitive 3D7 or multidrug resistant Dd2 were cultured in RPMI 1640 medium with 10% human serum and incubated for either 48 or 96 h in the presence of drug and [3H]-hypoxanthine. A 96 well plate with 0.2 mL of culture material per well at 0.2% parasitemia and 2-4% hematocrit, gives a radioactive incorporation signal of approximately 10,000 cpm at 48 h and 20,000 cpm at 96 h with background counts less than 500 cpm. Screening experiments were performed in duplicate and percent inhibition is reported as the average of two experiments.

TB: Literature Review

PI: Ballel, et al.
Published: 4/17/2009
TB Literature Data 49
Tuberculosis SAR data compiled in a survey of agents active against M. tuberculosis, including those with both known and unknown modes of action (Ballel, et al. “New Small-Molecule Synthetic Antimycobacterials” in Antimicrobial agents and chemotherapy, June 2005). Updated 4/17 with TubercuList/TBDB/other target links and improved references.

TB: Sacchettini et al., review

PI: Sean Ekins
Published: 2/18/2009
CDD – Sean Ekins 14
First and second line antituberculosis agents from Tables 1 and 2 in Sacchettini J.C., Rubin E.J. and Freundlich J.S. Drugs versus bugs: in pursuit of the persistent predator Mycobacterium tuberculosis, Nature Reviews Microbiology, 6, 41-52, (2008).

VENDOR: IUPUI – Distributed Drug Discovery (D3) Public Data

PI: M. J. O’Donnell and W. L. Scott
Published: 1/1/2009
IUPUI – D3 Enum 73K N-AcylAA-OH, -OMe, -NH2 48818
An open-access virtual catalog of acylated unnatural amino acids and their methyl esters. We encourage our colleagues to communicate with us concerning interest in the Distributed Drug Discovery project and synthetic methodology, which are described in a series of three papers in the Journal of Combinatorial Chemistry (in press).

VENDOR: ASINEX Building Blocks

PI: Mark Parisi
Published: 12/23/2008
Drug like Building Blocks, if you are considering a lead optimization program, our Building Blocks may prove to be exactly what you are looking for.


PI: Sean Ekins
Published: 12/21/2008
CDD – Sean Ekins 228
Molecule and structure name data for scents from a book by Roman Kaiser, “meaningful scents around the world” published by Wiley-VCH in 2006. Molecule number relates to their numbering in the book.

TOX: toxcast

PI: Sean Ekins
Published: 12/18/2008
CDD – Sean Ekins 306
EPA toxcast library of compounds (mostly pesticides) available at

FDA APPROVED, TOX: Maximum recommended daily dose

PI: Sean Ekins
Published: 12/10/2008
CDD – Sean Ekins 1215
An FDA database which contains maximum recommended daily dose values for over 1200 pharmaceuticals. The dataset represents some of the molecules used in the following publication Matthews, E.J., et al., Current Drug Discovery Technologies, 1(1): 61-76. (2004)

VENDOR: Ayurvedic Traditions vis-a-vis Current Healthcare & Wellness Needs

PI: Falguni Dasgupta
Published: 10/30/2008
Falguni Dasgupta: Personal Data Compilation 37
Traditional use of Indian medicinal plants and their extracts is discussed with reference to modern perspectives with the objective of finding common grounds, re-evaluation of claims and creating opportunities in Healthcare and Wellness in conformity with regulatory requirements as well as finding New Drug “Leads.”

PARASITES: Sandler-UCSF Celera Cysteine Protease Inhibitor Library

PI: Jim McKerrow
Published: 10/23/2008
McKerrow Group 1860
In vitro T. cruzi and T. brucei parasite and specific enzyme screens.

FDA APPROVED: Approved Drugs

PI: David Sullivan
Published: 10/16/2008
Johns Hopkins Clinical Compound Library 2815
FDA approved drugs with defined molecular structure including 763 molecules from the Physicians’ Desk Reference, 780 from DrugBank, 1151 in the Orange Book 2007, and 1007 from Dr. Chris Lipinski’s FDA list


PI: Mark Parisi
Published: 10/2/2008
High Quality exceptionally drug like GPCR oriented set available at a discounted rate to the CDD community. This library incorporates our medicinal chemistry expertise and our ability to identify privileged fragments from literature and assemble them in an unprecedented way.

GPCR: PDSP Ki Database

PI: Bryan Roth
Published: 9/16/2008
PDSP Ki Database 20026
Over 47,000 Ki values against 699 GPCR targets from the NIMH Psychoactive Drug Screening Program (PDSP) Database

VENDOR: ASINEX Synergy Libraries

PI: Mark Parisi
Published: 4/26/2008
ASINEX 25008
ASINEX has developed a new high diversity library rich in drug like pharmacophore fragments. The design of the library is based on two forms of Synergy. The first is the inter-relationship between diverse and targeted oriented techniques, and the second involves the convergence of multi-step key intermediates (6-9 steps) in order to create sophisticated compounds. See the PDF below for more details.

TOX: Structures with Known Toxicity Profiles’s Public Data

PI: Sean Ekins, PhD
Published: 3/28/2008
Structures with Known Toxicity Profiles 135
Tissue specific toxicity profiles of known compounds with references

PROMISCUOUS INHIBITORS: Shoichet published promiscuous inhibitors

PI: Brian Shoichet
Published: 3/26/2008
Shoichet published promiscuous inhibitors 111
Aggregates creating “false positives” by self-association of organic molecules in aqueous solutions

TOX: UC Davis – Hammock’s Public Data

PI: Bruce Hammock
Published: 3/17/2008
UC Davis – Hammock 714
Inhibitors of soluble epoxide hydrolases (sEH) – these enzymes have 3 main functions: detoxification, catabolism and regulation of signaling molecules.


PI: Kip Guy
Published: 3/5/2008
St. Jude – Malaria/Trypanosome Bioactives 2426
Open access results from Kip Guy’s laboratory at St. Jude Children’s Research Hospital including HTS of bioactives against malaria and T. brucei

MALARIA: Drexel Public Data

PI: Jean-Claude Bradley
Published: 3/2/2008
Drexel University 195
Results from an ongoing open data collaboration between
Drexel (Ugi-4CC products) and UCSF (antimalarial screening). This data set represents an example of how researchers can choose to publish selected results openly. (By default, in contrast, all groups are private.)

MALARIA: U.S. Army Survey

PI: Frederick Y. Wiselogle
Published: 2/29/2008
U.S. Army Malaria Literature Survey 12318
An extensive collection of antimalarial drug animal SAR data, including chemical structures, bioactivity data, pharmacological data, and toxicity data (Published originally by the U.S. Army in 1946 as “A Survey of Malaria Drugs”)


PI: David Roos
Published: 2/19/2008
UPenn – Malaria Literature Data 120
PlasmoDB of malaria inhibitors compiled from the literature, including chemical structure, PlasmoDB Gene Identifier, Target Gene Name, and references against P. falciparum, P. vivax, P. berghei, P. yoelii, P. chabaudi, P. vinckei petteri

MALARIA: Natural Products (NPPDB)

PI: Babu Tekwani
Published: 2/15/2008
National Center for Natural Products Research 426
Antimalarial database of flavone natural products, including antimalarial and cytotoxicity data (University of Mississippi, National Center for Natural Products Research)

TB: TAACF Assay Results

PI: Bernard Munos
Published: 2/12/2008
TB Early Phase Drug Discovery Program 812
Antibacterial activity of a publicly available library of 812 compounds against Mycobacterium tuberculosis (H37Rv) in Alamar Blue whole cell assay

FDA APPROVED: Orphan Drugs

PI: Christopher Lipinski
Published: 10/26/2007
Known drugs 1721
FDA approved drugs with designated indications, sponsor name and chemical structures (when available)

Translated with Google Translate