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License status and Mdexa hosting, recorded separatelyAll datasets

BindingDB

Verified by Mdexa · Checked against the source text under public rules.How we check

Commercial use
Yes
Derivatives
Yes
Redistribution
Yes
File on Mdexa
NoLink only

all parts permissive

PermissiveLink onlyCC-BY-3.0Save

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Mdexa verified · Permissive · 2026-11Mdexa verifiedPermissive · 2026-11

[![Mdexa verified · Permissive · 2026-11](https://mcp.mdexa.com/v1/badge/datasets/bindingdb.svg)](https://mdexa.com/datasets/bindingdb/)

Place it on a repository or dataset page; the status and date follow the verification. About badges

Cite this pageMdexa, BindingDB, https://mdexa.com/datasets/bindingdb/, verified 2026-11-14.

Source riskDerived

Key facts

Domain
Pharmacy and drugs Modern medicine
Content
DatabasesPublic web-accessible database of measured protein-ligand binding affinities between candidate drug-target proteins and small drug-like molecules, used in drug discovery and medicinal chemistry.
Size
—As stated: 3.2M data for 1.4M Compounds and 11.5K Targets
Language / modality
English / Tabular
Publisher
University of California San Diego (BindingDB)
Year
—
Expert review
—
Verification
Verified: license text seen

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)

Quoted statements and their sources are in BindingDB license evidence.

Verdicts record what sources state and are not legal advice.

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.org ·
    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 · Dataset page · checked 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.
    bindingdb.org ·
    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 · Dataset page · checked 2026-11-12

  • The data collection comes from measurement techniques including enzyme inhibition and kinetics, isothermal titration calorimetry, NMR, and radioligand and competition assays.
    bindingdb.org ·
    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 · Dataset page · checked 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.org ·
    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 · Dataset page · checked 2026-11-12

  • BindingDB also includes a small collection of host-guest binding data.
    bindingdb.org ·
    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 · Dataset page · checked 2026-11-12

Identifiers

  • BindingDB monomer (compound) IDBindingDB uses monomer (compound) IDs, which a download file maps to PubChem CIDs.
    bindingdb.org ·
    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 · Dataset page · checked 2026-11-13

  • BindingDB polymer (single protein) IDBindingDB uses polymer (single protein) IDs, mapped to UniProt IDs in a download file.
    bindingdb.org ·
    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 · Dataset page · checked 2026-11-13

  • → PubChem CIDsA download file maps BindingDB monomer (compound) IDs to PubChem CIDs.
    bindingdb.org ·
    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 · Dataset page · checked 2026-11-13

  • → PubChem SIDsA download file maps BindingDB monomer (compound) IDs to PubChem SIDs.
    bindingdb.org ·
    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 · Dataset page · checked 2026-11-13

  • → ChEBIA download file maps BindingDB monomer (compound) IDs to CHEBI IDs.
    bindingdb.org ·
    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 · Dataset page · checked 2026-11-13

  • → DrugBankA download file maps BindingDB monomer (compound) IDs to DrugBank IDs.
    bindingdb.org ·
    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 · Dataset page · checked 2026-11-13

  • → UniProtA download file maps BindingDB polymer (single protein) IDs to UniProt IDs.
    bindingdb.org ·
    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 · Dataset page · checked 2026-11-13

  • → PubMedA download file collects the PubMed IDs present in BindingDB.
    bindingdb.org ·
    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 · Dataset page · checked 2026-11-13

Access

Versions

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.
    pmc.ncbi.nlm.nih.gov ·
    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/ · peer-reviewed-paper · checked 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.
    pmc.ncbi.nlm.nih.gov ·
    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/ · peer-reviewed-paper · checked 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.
    pmc.ncbi.nlm.nih.gov ·
    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/ · peer-reviewed-paper · checked 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.org ·
    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 · Dataset page · checked 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.
    bindingdb.org ·
    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 · Dataset page · checked 2026-11-12

Tags

Intended use
Evaluation

Quoted from the sourceTo 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.Snapshot s02

Specialty
Pharmacy
Source type
Research literature

Quoted from the sourceBindingDB includes data extracted from the literature and patents by the BindingDB projectSnapshot s02

Built from a knowledge base

Quoted from the sourceBindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding dataSnapshot s02

Expert involvement
Per-item review
Data format
TSV

Author-statedInferredHuman-confirmed

BindingDB license evidence 4

Conditions are the union of the parts

  1. Terms of use pagePage opened
    Third-party text · Terms of use pageData imported from ChEMBL are provided under their Creative Commons Attribution-Share Alike 3.0 Unported License .

    Statement found in snapshot s02 (page)

    bindingdb.org2026-11-12 · s02
  2. Terms of use pagePage opened
    Third-party text · Terms of use pageAll data curated by BindingDB staff are provided under the Creative Commons Attribution 3.0 License .

    Statement found in snapshot s02 (page)

    bindingdb.org2026-11-12 · s02
  3. Dataset pagePage opened
    Third-party text · Dataset pageData imported from ChEMBL are provided under their Creative Commons Attribution-Share Alike 3.0 Unported License

    Part "data imported from ChEMBL" found in snapshot s02 (page)

    bindingdb.org2026-11-12 · s02
  4. Dataset pagePage opened
    Third-party text · Dataset pageAll data curated by BindingDB staff are provided under the Creative Commons Attribution 3.0 License

    Part "data curated by BindingDB staff" found in snapshot s02 (page)

    bindingdb.org2026-11-12 · s02

Source and lineage

  • Derived fromChEMBLnot in the database
  • Derived fromPubChem confirmatory BioAssaysnot in the database

Known issues with BindingDB

—

Preflight

Not run Runs only on ingested data; says nothing about quality.

Downloading BindingDB and API access

No file on Mdexa (see the verdict). Get it from the source and confirm the terms there:

Citing BindingDB

Mdexa, BindingDB, https://mdexa.com/datasets/bindingdb/, verified 2026-11-14.
More citation details

The source gives no citation text; the line above cites this card.

Machine-readable

bindingdb.jsonbindingdb.mdcatalog.json

Change log 37
2026-11-14Known 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.
2026-11-14Practical fields (scope, identifiers, access methods, versions, known defects) were added by the automated pipeline from stored page snapshots; every statement carries a verbatim quote.
2026-11-14Known 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.
2026-11-14Known 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.
2026-11-14Re-adjudicated under the current rules; all machine checks still pass.
2026-11-14Known 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.
2026-11-14Known 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.
2026-11-14Re-adjudicated under the current rules; all machine checks still pass.
2026-11-14Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Re-adjudicated under the current rules; all machine checks still pass.
2026-11-13Re-adjudicated under the current rules; all machine checks still pass.
2026-11-13Re-adjudicated under the current rules; all machine checks still pass.
2026-11-13Re-adjudicated under the current rules; all machine checks still pass.
2026-11-13Re-adjudicated under the current rules; all machine checks still pass.
2026-11-13Re-adjudicated under the current rules; all machine checks still pass.
2026-11-13Re-adjudicated under the current rules; all machine checks still pass.
2026-11-13Re-adjudicated under the current rules; all machine checks still pass.
2026-11-13Added via the automated pipeline and passed all checks (gates, verbatim quotes, rule engine, two independent extractions).

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