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Datasets

D3R is working to assemble and augment informative, high-quality datasets for validation and improvement of methods in computer-aided drug design. Ideally, a single dataset will be comprised of 25 or more congeneric compounds, 5 – 10 co-crystal structures, related affinity data and a number of known inactive compounds. Current sources for our datasets are pharmaceutical companies and academic collaborators.

The data contributors, D3R, and UC San Diego are not liable for, and expressly exclude, all liability for loss or damage however and whenever caused to any user of these data. This exclusion of liability includes, but is not limited to, any special, incidental, consequential, punitive, or exemplary damages. If liability may not be excluded by law, it is limited to actual and direct financial loss to the extent and proportionality it is caused by proved negligence on the part of these parties.

In any publication, presentation or other public disclosure of these data, users are expected to cite D3R and acknowledge the source(s) of the data used. To cite D3R, please list "D3R" or "Drug Design Data Resource" and provide the URL drugdesigndata.org.

Name TargetCompoundsInactivesPDBsPhysical PropertiesITCSource # of Files # of Documents Added
Drug Design Data Resource Grand Challenge 2 Dataset: FXR - Farnesoid X ReceptorThe Farnesoid X receptor (FXR) dataset, contributed by Roche, comprises 36 co-crystal structures of FXR with chemically varied ligands, one apo structure, and 102 IC50s measured with a Scintillation Proximity Assay. Among these compounds, 96 belong to four chemical series (benzimidazoles, isoxazoles, spiros and sulfonamides) and six are classified as miscellaneous. For 92 of the compounds, IC50 values range from 0.000335 to 62.37 µM, while the remaining ten IC50s are greater than 100 µM. Some of the compounds were synthesized as racemates, diastereomers and epimers, as noted within the dataset. The 37 co-crystal and apo structures have resolutions ranging from 1.8 to 2.6 Å and contain representatives from each of the four chemical series. (http://dx.doi.org/10.15782/D6RP4P)FXR1021036yesnoRoche1110:57am April 13, 2017
Genentech MAP4K4The MAP4K4 dataset, kindly donated by Genentech, has been curated by D3R. This kinase, a member of the STE20 family, is involved in a number of pathways that are important to drug discovery, metabolism, cancer and inflammation. (http://dx.doi.org/10.15782/D6WC7Z)MAP4K433yesnoGenentech1009:02am September 2, 2016
AbbVie-CSAR HSP90The HSP90 dataset, kindly donated by Abbvie, was expanded and curated by the CSAR group at University of Michigan. The ATP site of HSP90 has been the subject of many oncology drug discovery programs over the past 15 years and consequently has a large representation in the PDB and literature. However, the prevalence of water-mediated ligand protein-interactions and a ligand binding site that accesses multiple open and closed pocket conformations can make estimation of docking pose and ranked affinity a challenge. (http://dx.doi.org/10.15782/D6159W)HSP901928yesnoAbbVie-CSAR1008:54am September 2, 2016
Baker-CSAR DIG-BPThis dataset was originally donated by the Baker group and published by the Community Structure-Activity Resource (CSAR).DIG-BP10nonoBaker-CSAR1011:19am July 29, 2015
GSK FactorXA-2This dataset was originally donated by GSK and published by the Community Structure-Activity Resource (CSAR).FactorXA-2717nonoGSK1010:36am July 29, 2015
GSK FactorXA-1This dataset was originally donated by GSK and published by the Community Structure-Activity Resource (CSAR).FactorXA-145nonoGSK1010:35am July 29, 2015
Abbott UrokinaseThis dataset was originally donated by Abbott and published by the Community Structure-Activity Resource (CSAR). See http://dx.doi.org/10.1021/ci4000486Urokinase4697yesnoAbbott1007:45am June 30, 2015
GSK TrmDThis dataset was originally donated by GSK and published by the Community Structure-Activity Resource (CSAR).TrmD3130nonoGSK1007:44am June 30, 2015
GSK SYK KinaseThis dataset was originally donated by GSK and published by the Community Structure-Activity Resource (CSAR).SYK Kinase2768nonoGSK1007:43am June 30, 2015
CSAR LpxCThis dataset was originally developed and published by the Community Structure-Activity Resource (CSAR). See http://dx.doi.org/10.1021/ci4000486LpxC32125yesyesCSAR1007:42am June 30, 2015
Sacchettini GlcBThis dataset was originally donated by the Sancchettini laboratory and published by the Community Structure-Activity Resource (CSAR). See http://dx.doi.org/10.1016/j.chembiol.2012.09.018GlcB1975nonoSacchettini1007:40am June 30, 2015
Vertex ERK2This dataset was originally donated by Vertex and published by the Community Structure-Activity Resource (CSAR). See dx.doi.org/10.1021/ci4000486ERK229810nonoVertex1007:38am June 30, 2015
Abbott CHK1 KinaseThis dataset was originally donated by Abbott and published by the Community Structure-Activity Resource (CSAR). See http://dx.doi.org/10.1021/ci4000486CHK1 Kinase1373013nonoAbbott1007:36am June 30, 2015
CSAR CDK2 KinaseThis dataset was originally developed and published by the Community Structure-Activity Resource (CSAR). See http://dx.doi.org/10.1021/ci4000486CDK2 Kinase1118519yesyesCSAR1007:32am June 30, 2015
CSAR CDK2-CyclinAThis dataset was originally developed and published by the Community Structure-Activity Resource (CSAR). See http://dx.doi.org/10.1021/ci4000486CDK2-CyclinA111851yesyesCSAR1007:31am June 30, 2015
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