# BindingDB License: permissive, share-alike (CC-BY-3.0); Mdexa hosting: link-only. all parts permissive; conditions are the union of the parts Risk flag(s): derived. - Commercial use: Yes · Derivatives: Yes · Redistribution: Yes · File on Mdexa: No - License status: Permissive (CC-BY-3.0) - Mdexa hosting: Link only — License permissive, share-alike: all parts permissive; conditions are the union of the parts. Risk flag(s): derived. Link only. - Source risk: Derived - Last verified: 2026-11-14 - Card: https://mdexa.com/datasets/bindingdb/ ## Key facts - Domain: Pharmacy and drugs - Content type: Databases - Size: — — 3.2M data for 1.4M Compounds and 11.5K Targets - Language: English - Modality: Tabular - Publisher: University of California San Diego (BindingDB) - Year: — ## Commercial use of BindingDB - Commercial use: Yes. The overall verdict takes the strictest part; the parts carry different licenses, listed below. - License status: Permissive. - Conditions: Attribution, Share-alike - License part: Data imported from ChEMBL — Permissive (CC-BY-SA-3.0) - License part: data curated by BindingDB staff — Permissive (CC-BY-3.0) Verdicts record what sources state and are not legal advice. ## BindingDB license evidence all parts permissive; conditions are the union of the parts - **Terms of use page**: Statement found in snapshot s02 (page) — "Data imported from ChEMBL are provided under their Creative Commons Attribution-Share Alike 3.0 Unported License ." — https://www.bindingdb.org/rwd/bind/info.jsp (2026-11-12; Page opened) - **Terms of use page**: Statement found in snapshot s02 (page) — "All data curated by BindingDB staff are provided under the Creative Commons Attribution 3.0 License ." — https://www.bindingdb.org/rwd/bind/info.jsp (2026-11-12; Page opened) - **Dataset page**: Part "data imported from ChEMBL" found in snapshot s02 (page) — "Data imported from ChEMBL are provided under their Creative Commons Attribution-Share Alike 3.0 Unported License" — https://www.bindingdb.org/rwd/bind/info.jsp (2026-11-12; Page opened) - **Dataset page**: Part "data curated by BindingDB staff" found in snapshot s02 (page) — "All data curated by BindingDB staff are provided under the Creative Commons Attribution 3.0 License" — https://www.bindingdb.org/rwd/bind/info.jsp (2026-11-12; Page opened) ## Source and lineage — - Derived from: ChEMBL - Derived from: PubChem confirmatory BioAssays ## Known issues with BindingDB — ## Preflight Not run (data not ingested). ## Downloading BindingDB and API access Mdexa does not serve files. Original source: - https://www.bindingdb.org/ - https://www.bindingdb.org/rwd/bind/info.jsp ### Access recipe - API getLigandsByUniprot: `https://bindingdb.org/rest/getLigandsByUniprot?uniprot={UNIPROT};{IC50cutoff}` · example `https://bindingdb.org/rest/getLigandsByUniprot?uniprot=P35355;100&response=application/json` ## Citing BindingDB No recommended citation text. ## Machine-readable - JSON: https://mdexa.com/datasets/bindingdb.json - 2026-11-14 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-14 Practical fields (scope, identifiers, access methods, versions, known defects) were added by the automated pipeline from stored page snapshots; every statement carries a verbatim quote. - 2026-11-14 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-14 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-14 Re-adjudicated under the current rules; all machine checks still pass. - 2026-11-14 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-14 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-14 Re-adjudicated under the current rules; all machine checks still pass. - 2026-11-14 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Re-adjudicated under the current rules; all machine checks still pass. - 2026-11-13 Re-adjudicated under the current rules; all machine checks still pass. - 2026-11-13 Re-adjudicated under the current rules; all machine checks still pass. - 2026-11-13 Re-adjudicated under the current rules; all machine checks still pass. - 2026-11-13 Re-adjudicated under the current rules; all machine checks still pass. - 2026-11-13 Re-adjudicated under the current rules; all machine checks still pass. - 2026-11-13 Re-adjudicated under the current rules; all machine checks still pass. - 2026-11-13 Re-adjudicated under the current rules; all machine checks still pass. - 2026-11-13 Added via the automated pipeline and passed all checks (gates, verbatim quotes, rule engine, two independent extractions). ## Practical information ### Content scope - BindingDB holds about 3,241,782 binding data records covering 11,509 proteins and over 1,440,011 drug-like molecules. > BindingDB currently contains about 3,241,782 binding data for 11,509 proteins and over 1,440,011 drug-like molecules. https://www.bindingdb.org/rwd/bind/info.jsp (2026-11-12) - Of that total, 1.6 million data records for 772 thousand compounds and 4.8 thousand targets were curated by BindingDB curators. > Of those, 1.6M data for 772K Compounds and 4.8K Targets were curated by BindingDB curators. https://www.bindingdb.org/rwd/bind/info.jsp (2026-11-12) - The data collection comes from measurement techniques including enzyme inhibition and kinetics, isothermal titration calorimetry, NMR, and radioligand and competition assays. > The data collection derives from a variety of measurement techniques, including enzyme inhibition and kinetics, isothermal titration calorimetry, NMR, and radioligand and competition assays. https://www.bindingdb.org/rwd/bind/info.jsp (2026-11-12) - BindingDB includes data extracted from literature and patents by the project, selected PubChem confirmatory BioAssays, and ChEMBL entries with a well defined protein target. > BindingDB includes data extracted from the literature and patents by the BindingDB project, selected PubChem confirmatory BioAssays, and ChEMBL entries for which a well defined protein target ("TARGET_TYPE='PROTEIN'") is provided. https://www.bindingdb.org/rwd/bind/info.jsp (2026-11-12) - BindingDB also includes a small collection of host-guest binding data. > BindingDB also includes a small collection of host-guest binding data of interest to chemists studying supramolecular systems. https://www.bindingdb.org/rwd/bind/info.jsp (2026-11-12) ### Identifiers - BindingDB uses monomer (compound) IDs, which a download file maps to PubChem CIDs. > BindingDB_CID.txt ( Mapping of BindingDB monomer (compound) IDs to PubChem CIDs. 23.67 MB, updated 2026-10-01) https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp (2026-11-13) - BindingDB uses polymer (single protein) IDs, mapped to UniProt IDs in a download file. > BindingDB_UniProt.txt ( Mapping of BindingDB polymer (single protein) IDs to UniProt IDs. 572.93 KB, updated 2026-10-01) https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp (2026-11-13) - A download file maps BindingDB monomer (compound) IDs to PubChem CIDs. > BindingDB_CID.txt ( Mapping of BindingDB monomer (compound) IDs to PubChem CIDs. 23.67 MB, updated 2026-10-01) https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp (2026-11-13) - A download file maps BindingDB monomer (compound) IDs to PubChem SIDs. > BindingDB_SID.txt ( Mapping of BindingDB monomer (compound) IDs to PubChem SIDs. 24.44 MB, updated 2026-10-01) https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp (2026-11-13) - A download file maps BindingDB monomer (compound) IDs to CHEBI IDs. > BindingDB_CHEBI_ID.txt ( Mapping of BindingDB monomer (compound) IDs to CHEBI IDs. 191.64 KB, updated 2026-10-01) https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp (2026-11-13) - A download file maps BindingDB monomer (compound) IDs to DrugBank IDs. > BindingDB_DrugBankID.txt ( Mapping of BindingDB monomer (compound) IDs to DrugBank IDs. 41.02 KB, updated 2026-10-01) https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp (2026-11-13) - A download file maps BindingDB polymer (single protein) IDs to UniProt IDs. > BindingDB_UniProt.txt ( Mapping of BindingDB polymer (single protein) IDs to UniProt IDs. 572.93 KB, updated 2026-10-01) https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp (2026-11-13) - A download file collects the PubMed IDs present in BindingDB. > BindingDB_PubMed.txt ( Collection of PubMed IDs in BindingDB. 396.56 KB, updated 2026-11-13) https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp (2026-11-13) ### Access - Web API: https://www.bindingdb.org/rwd/bind/BindingDBRESTfulAPI.jsp - Bulk download: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp - Database dump: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp - Database dump: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?all_download=yes - Web interface only: https://pmc.ncbi.nlm.nih.gov/articles/PMC11701568/ ### Versions - The 202611 release file BindingDB_All_202611_tsv.zip is marked as updated 2026-10-31. > BindingDB_All_202611_tsv.zip ( 566.75 MB, updated 2026-10-31 ) md5 https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp (2026-11-13) - The download files are updated when new data are added, usually monthly. > These files updated when new data are added, usually monthly https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp (2026-11-13) - The Oracle database dump BDB-Oracle_All_202502_dmp.zip is listed as Discontinued. > Full BindingDB Database Dump Oracle DB: BDB-Oracle_All_202502_dmp.zip (Discontinued) ( 837.50 MB, updated 2025-03-26) md5 https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp (2026-11-13) ### Known defects and misuse - BindingDB authors: the most common curation error (by BindingDB or ChEMBL) is a factor-of-1000 unit error, e.g. an IC50 curated as nM instead of µM. > These appear most commonly as a factor of 1000 error resulting from miscuration of e.g. an IC50 value as nanomolar instead of micromolar or vice versa . https://pmc.ncbi.nlm.nih.gov/articles/PMC11701568/ (2026-11-13) - BindingDB authors: the next most common reported error is misidentification of the protein target, usually when a document covers multiple targets or subtypes. > Based on user feedback, the next most common error appears to be misidentification of a protein target. https://pmc.ncbi.nlm.nih.gov/articles/PMC11701568/ (2026-11-13) - Errors in source patents or articles are hard for BindingDB to detect; they may show up only as outliers when the same affinity was measured more than once. > Such errors are difficult for us to discover and hence correct, though they might be flagged as outliers in cases where the same protein-ligand affinity has been measured more than once. https://pmc.ncbi.nlm.nih.gov/articles/PMC11701568/ (2026-11-13) ### Suited for - BindingDB states it supports medicinal chemistry and drug discovery through literature awareness and SAR/QSAR development, and validation of computational approaches such as docking, scoring and free energy methods. > BindingDB supports medicinal chemistry and drug discovery via literature awareness and development of structure-activity relations (SAR and QSAR); validation of computational chemistry and molecular modeling approaches such as docking, scoring and free energy methods https://www.bindingdb.org/rwd/bind/info.jsp (2026-11-12) - BindingDB downloads and search results provide the publication date and BindingDB curation date of each measurement to help with training and testing AI and other models. > To help with training and testing AI and other models, BindingDB downloads and search results now provide the publication date and BindingDB curation date of each measurement. https://www.bindingdb.org/rwd/bind/info.jsp (2026-11-12) ### No sourced statement yet Unsuited tasks, Commercial licensing ## Continue in this database This record is one of 109 processed and verified records (datasets, data resources and open models). To find others, call `https://mcp.mdexa.com/v1/datasets?q=` or connect the MCP server at `https://mcp.mdexa.com/mcp`; no key is needed for 20 calls per minute. Rows are under 1 KB; an empty result means "not listed". For a list of items, one batch check (free account) returns a report. Guide: /agents.md. Similar records: TopU-LBVS: Multi-Target Benchmark for Ligand-Based Virtual Screening (https://mdexa.com/datasets/topu-lbvs/); Therapeutics Data Commons (https://mdexa.com/datasets/tdc/); ChEMBL (https://mdexa.com/datasets/chembl/).