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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 | Description | Target | Compounds | Inactives | PDBs | Physical Properties | ITC | Source | # of Files | # of Documents | Added |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Drug Design Data Resource Grand Challenge 4 Dataset: CathepsinS | The cathepsins constitute an 11-member family of proteases involved in protein degradation. Cathepsin S is highly expressed in antigen-presenting cells, where it degrades major histocompatibility complex class II (MHC II)-associated invariant chain. CatS is a candidate target for regulating immune hyper-responsiveness, as the inhibition of CatS may limit antigen presentation. This data set comprises a follow-on challenge to GC3, consisting of non-peptidic, non-covalent, small molecule inhibitors across a three order of magnitude range (nM to μM) of IC50s for CatS. Specifically, we provide 459 CatS inhibitors for affinity prediction, and 39 molecules for free energy prediction. This dataset was kindly donated by Janssen. Please note the affinity values from this set were measured against a C25S CatS mutant. | Cathepsin S | 459 | _ | _ | no | Janssen | 1 | 0 | 01:59pm February 6, 2020 | |
| Drug Design Data Resource Grand Challenge 4 Dataset: BACE1 | Beta-Secretase 1 (BACE) is a transmembrane aspartic-acid protease human protein encoded by the BACE1 gene. BACE is essential for the generation of beta-amyloid peptide in neural tissue, a component of amyloid plaques widely believed to be critical in the development of Alzheimer's, rendering BACE an attractive therapeutic target for this devastating disease. The BACE dataset provided herein comprises small molecule inhibitors across a three order of magnitude (nM to μM) range of IC50s along with previously undisclosed crystallographic structures. Specifically, we provide 154 BACE inhibitors for affinity, 20 for pose, and 34 for free energy prediction. This dataset was kindly provided by Novartis. | BACE1 | 154 | _ | 20 | _ | no | Novartis | 1 | 0 | 01:59pm February 6, 2020 |
| Drug Design Data Resource Grand Challenge 3 Dataset: ABL1 | ABL1 is a protein tyrosine kinase that is implicated in various cancers, including in chronic myelogenous leukemia (CML), through fusion of the ABL gene, in chromosome 9, and the BCR gene, in chromosome 22. This subchallenge tests the ability of computational methods to predict the effect of target mutations on small molecule binding affinities. The dataset consists of Kd values for two compounds versus the wild type and five mutants of the nonphosphorylated ABL1 protein, ABL1(F317I), ABL1(F317L), ABL1(H396P), ABL1(Q252H), and ABL1(T315I). | ABL1 | 10 | _ | _ | no | 1 | 0 | 01:58pm February 6, 2020 | ||
| Drug Design Data Resource Grand Challenge 3 Dataset: TIE2 | Angiopoietin-1 receptor (TIE2) is composed of an extracellular domain for ligand binding, a transmembrane domain, and a cytoplasmic tyrosine kinase domain. For this challenge, we focus on the cytoplasmic kinase domain which is a tyrosine kinase involved in tumor-induced angiogenesis. This is an affinity ranking/scoring, and free energy challenge, designed to test the ability of current methods to detect large changes in affinity due to small changes in chemical structure. The dataset comprises 18 congeneric ligands with Kd values for the kinase TIE2. From this full set of 18, two free energy subsets of 4 and 6 compounds were selected as amenable to alchemical relative binding free energy calculations. | TIE2 | 18 | _ | _ | no | 1 | 0 | 01:57pm February 6, 2020 | ||
| Drug Design Data Resource Grand Challenge 3 Dataset: JAK2_SC3 | Janus Kinase 2 (JAK2) is an intracellular protein tyrosine kinase that is critical to the mediation of cytokine signaling. Its dysregulation is involved in multiple diseases, including autoimmune diseases (rheumatoid arthritis and psoriasis), myeloproliferative syndromes (polycythemia vera, leukemias, and lymphomas), and cardiovascular diseases. This is an affinity ranking/scoring, and free energy challenge, designed to test the ability of current methods to detect large changes in affinity due to small changes in chemical structure. The dataset comprises 17 congeneric compounds with Kd values for the kinase JAK2. Note that the chiral compounds were measured as racemates. | JAK2 | 17 | _ | _ | no | 1 | 0 | 01:57pm February 6, 2020 | ||
| Drug Design Data Resource Grand Challenge 3 Dataset: p38a | p38-?, also called mitogen-activating protein kinase 14 (MAPK14), is part of the MAP kinase family, which function as serine/threonine kinases that mediate intracellular signal transduction pathways. p38-? has been of particular interest to pharmaceutical companies as a potential target for the treatment of arthritic and inflammatory diseases. It is based on dissociation constants (Kd) for 72 diverse ligands. | p38a | 72 | _ | _ | no | 1 | 0 | 01:56pm February 6, 2020 | ||
| Drug Design Data Resource Grand Challenge 3 Dataset: JAK2_SC2 | Janus Kinase 2 (JAK2) is an intracellular protein tyrosine kinase that is critical to the mediation of cytokine signaling. Its dysregulation is involved in multiple diseases, including autoimmune diseases (rheumatoid arthritis and psoriasis), myeloproliferative syndromes (polycythemia vera, leukemias, and lymphomas), and cardiovascular diseases. It is based on dissociation constants (Kd) for 89 diverse ligands. | JAK2 | 89 | _ | _ | no | 1 | 0 | 01:55pm February 6, 2020 | ||
| Drug Design Data Resource Grand Challenge 3 Dataset: VEGFR2 | Vascular endothelial growth factor receptor 2 (VEGFR2) is fundamental for vascular endothelial cell development. It is involved in tumor angiogenesis and diabetic retinopathy. The tyrosine kinase domain of VEGFR-2 has been an attractive drug target for a number of pharmaceutical companies with the aim to block its downstream intracellular signaling pathways. This effort has resulted in multiple tyrosine kinase inhibitors. It is based on dissociation constants (Kd) for 85 diverse ligands. | VEGFR2 | 85 | _ | _ | no | 1 | 0 | 01:54pm February 6, 2020 | ||
| Drug Design Data Resource Grand Challenge 3 Dataset: CathepsinS | The cathepsins constitute an 11-member family of proteases involved in protein degradation. Cathepsin S is highly expressed in antigen-presenting cells, where it degrades major histocompatiability complex class II (MHC II)-associated invariant chain. CatS is a candidate target for regulating immune hyper-responsiveness, as the inhibition of CatS may limit antigen presentation. This data set comprises non-peptidic, non-covalent, small molecule inhibitors across a three order of magnitude range (nM to μM) of IC50s for CatS. Specifically, we provide 136 CatS inhibitors for affinity prediction, 24 for pose prediction, and 33 for free energy prediction. | Cathepsin S | 136 | _ | 24 | _ | no | Janssen | 1 | 0 | 01:52pm February 6, 2020 |
| Drug Design Data Resource Grand Challenge 2 Dataset: FXR - Farnesoid X Receptor | The 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) | FXR | 102 | 10 | 36 | yes | no | Roche | 1 | 1 | 10:57am April 13, 2017 |
| Genentech MAP4K4 | The 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) | MAP4K4 | 33 | yes | no | Genentech | 1 | 0 | 09:02am September 2, 2016 | ||
| AbbVie-CSAR HSP90 | The 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) | HSP90 | 192 | 8 | yes | no | AbbVie-CSAR | 1 | 0 | 08:54am September 2, 2016 | |
| Baker-CSAR DIG-BP | This dataset was originally donated by the Baker group and published by the Community Structure-Activity Resource (CSAR). | DIG-BP | 10 | no | no | Baker-CSAR | 1 | 0 | 11:19am July 29, 2015 | ||
| GSK FactorXA-2 | This dataset was originally donated by GSK and published by the Community Structure-Activity Resource (CSAR). | FactorXA-2 | 71 | 7 | no | no | GSK | 1 | 0 | 10:36am July 29, 2015 | |
| GSK FactorXA-1 | This dataset was originally donated by GSK and published by the Community Structure-Activity Resource (CSAR). | FactorXA-1 | 45 | no | no | GSK | 1 | 0 | 10:35am July 29, 2015 | ||
| Abbott Urokinase | This dataset was originally donated by Abbott and published by the Community Structure-Activity Resource (CSAR). See http://dx.doi.org/10.1021/ci4000486 | Urokinase | 46 | 9 | 7 | yes | no | Abbott | 1 | 0 | 07:45am June 30, 2015 |
| GSK TrmD | This dataset was originally donated by GSK and published by the Community Structure-Activity Resource (CSAR). | TrmD | 31 | 30 | no | no | GSK | 1 | 0 | 07:44am June 30, 2015 | |
| GSK SYK Kinase | This dataset was originally donated by GSK and published by the Community Structure-Activity Resource (CSAR). | SYK Kinase | 276 | 8 | no | no | GSK | 1 | 0 | 07:43am June 30, 2015 | |
| CSAR LpxC | This dataset was originally developed and published by the Community Structure-Activity Resource (CSAR). See http://dx.doi.org/10.1021/ci4000486 | LpxC | 32 | 12 | 5 | yes | yes | CSAR | 1 | 0 | 07:42am June 30, 2015 |
| Sacchettini GlcB | This 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.2012.09.018 | GlcB | 19 | 7 | 5 | no | no | Sacchettini | 1 | 0 | 07:40am June 30, 2015 |
| Vertex ERK2 | This dataset was originally donated by Vertex and published by the Community Structure-Activity Resource (CSAR). See dx.doi.org/10.1021/ci4000486 | ERK2 | 298 | 10 | no | no | Vertex | 1 | 0 | 07:38am June 30, 2015 | |
| Abbott CHK1 Kinase | This dataset was originally donated by Abbott and published by the Community Structure-Activity Resource (CSAR). See http://dx.doi.org/10.1021/ci4000486 | CHK1 Kinase | 137 | 30 | 13 | no | no | Abbott | 1 | 0 | 07:36am June 30, 2015 |
| CSAR CDK2 Kinase | This dataset was originally developed and published by the Community Structure-Activity Resource (CSAR). See http://dx.doi.org/10.1021/ci4000486 | CDK2 Kinase | 111 | 85 | 19 | yes | yes | CSAR | 1 | 0 | 07:32am June 30, 2015 |
| CSAR CDK2-CyclinA | This dataset was originally developed and published by the Community Structure-Activity Resource (CSAR). See http://dx.doi.org/10.1021/ci4000486 | CDK2-CyclinA | 111 | 85 | 1 | yes | yes | CSAR | 1 | 0 | 07:31am June 30, 2015 |
About
Welcome to the Drug Design Data Resource Community. D3R is funded in part by NIH grant 1U01GM111528 from the National Institute of General Medical Sciences
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