BDB Download

Downloads

These files updated when new data are added, usually monthly

Many users find the tab-separated value (TSV) files easiest to work with. These have one row for each binding measurement, so each row has the SMILES string of a ligand, and these files can easily be loaded into spreadsheet programs like Excel and LibreOffice Calc. Detailed documentation is available for our TSV and SDfile formats.
If you have special requirements or suggestions, please contact us. We will do our best to help.

Full BindingDB Database Dump
- Oracle DB: BDB-Oracle_All_202410_dmp.zip ( 818.38 MB, updated 2024-10-01) md5
- MySQL DB: BDB-mySQL_All_202410_dmp.zip ( 795.49 MB, updated 2024-10-01) md5
Purchasable Compounds by Target
For each Target, this file (purchase_target_10000.tsv: 21.21 MB, updated 2024-09-29) lists all purchasable compounds we know of having affinity better than 10 uM, along with catalog links and pricing. Targets with no compounds like this are omitted. Contact us if you would like similar files with different cutoff criteria.
Ligand-Target-Affinity Datasets*
- All data in BindingdDB (2,928,077 measurements, 1,270,534 compounds, 9,347 targets)
  - BindingDB_All_2D_202410_sdf.zip ( 1.37 GB, updated 2024-09-29 ) md5
  - BindingDB_All_3D_202410_sdf.zip ( 2.69 GB, updated 2024-09-29 ) md5
  - BindingDB_All_202410_tsv.zip ( 472.04 MB, updated 2024-09-29 ) md5
- Only data curated from articles by BindingDB
  - BindingDB_BindingDB_Articles_2D_202410_sdf.zip ( 35.39 MB, updated 2024-09-29 ) md5
  - BindingDB_BindingDB_Articles_3D_202410_sdf.zip ( 83.36 MB, updated 2024-09-29 ) md5
  - BindingDB_BindingDB_Articles_202410_tsv.zip ( 16.51 MB, updated 2024-09-29 ) md5
- Only data in BindingDB drawn from ChEMBL
  - BindingDB_ChEMBL_2D_202410_sdf.zip ( 849.68 MB, updated 2024-09-29 ) md5
  - BindingDB_ChEMBL_3D_202410_sdf.zip ( 1.53 GB, updated 2024-09-29 ) md5
  - BindingDB_ChEMBL_202410_tsv.zip ( 278.18 MB, updated 2024-09-29 ) md5
- Only data in BindingDB drawn from Patents
  - BindingDB_Patents_2D_202410_sdf.zip ( 384.27 MB, updated 2024-09-29 ) md5
  - BindingDB_Patents_3D_202410_sdf.zip ( 894.89 MB, updated 2024-09-29 ) md5
  - BindingDB_Patents_202410_tsv.zip ( 123.25 MB, updated 2024-09-29 ) md5
- Only data in BindingDB drawn from PubChem
  - BindingDB_PubChem_2D_202410_sdf.zip ( 63.23 MB, updated 2024-09-29 ) md5
  - BindingDB_PubChem_3D_202410_sdf.zip ( 107.20 MB, updated 2024-09-29 ) md5
  - BindingDB_PubChem_202410_tsv.zip ( 24.13 MB, updated 2024-09-29 ) md5
- Only data in BindingDB drawn from PDSP Ki
  - BindingDB_PDSPKi_2D_202410_sdf.zip ( 15.93 MB, updated 2024-09-29 ) md5
  - BindingDB_PDSPKi_3D_202410_sdf.zip ( 36.23 MB, updated 2024-09-29 ) md5
  - BindingDB_PDSPKi_202410_tsv.zip ( 4.96 MB, updated 2024-09-29 ) md5
- Only CSAR data in BindingDB
  - BindingDB_CSAR_2D_202410_sdf.zip ( 349.85 KB, updated 2024-09-29 ) md5
  - BindingDB_CSAR_3D_202410_sdf.zip ( 708.33 KB, updated 2024-09-29 ) md5
  - BindingDB_CSAR_202410_tsv.zip ( 121.94 KB, updated 2024-09-29 ) md5
- Covid-19 data in BindingDB
  - BindingDB_Covid-19_2D_202410_sdf.zip ( 16.31 MB, updated 2024-09-29 ) md5
  - BindingDB_Covid-19_3D_202410_sdf.zip ( 26.47 MB, updated 2024-09-29 ) md5
  - BindingDB_Covid-19_202410_tsv.zip ( 6.16 MB, updated 2024-09-29 ) md5
- Only data in BindingDB directly provided by Prof. Palmer Taylor, UCSD
  - BindingDB_PTaylorLab_UCSD_2D_202410_sdf.zip ( 8.17 KB, updated 2024-09-29 ) md5
  - BindingDB_PTaylorLab_UCSD_3D_202410_sdf.zip ( 12.88 KB, updated 2024-09-29 ) md5
  - BindingDB_PTaylorLab_UCSD_202410_tsv.zip ( 3.34 KB, updated 2024-09-29 ) md5
- Only isothermal titration calorimetry (ITC) data in BindingDB
  - BindingDB_ITC_2D_202410_sdf.zip ( 504.62 KB, updated 2024-09-29 ) md5
  - BindingDB_ITC_3D_202410_sdf.zip ( 989.66 KB, updated 2024-09-29 ) md5
  - BindingDB_ITC_202410_tsv.zip ( 149.61 KB, updated 2024-09-29 ) md5
- Only data of host-guest systems in BindingDB
  - BindingDB_HostGuest_2D_202410_sdf.zip ( 180.58 KB, updated 2024-09-29 ) md5
  - BindingDB_HostGuest_3D_202410_sdf.zip ( 394.68 KB, updated 2024-09-29 ) md5
  - BindingDB_HostGuest_202410_tsv.zip ( 84.29 KB, updated 2024-09-29 ) md5
Lists and identifier mappings
- BindingDBTargetSequences.fasta ( FASTA format protein sequences of all protein Targets in BindingDB. 5.83 MB, updated 2024-09-29)
- BindingDB_CID.txt ( Mapping of BindingDB monomer (compound) IDs to PubChem CIDs. 20.73 MB, updated 2024-09-29)
- BindingDB_SID.txt ( Mapping of BindingDB monomer (compound) IDs to PubChem SIDs. 21.51 MB, updated 2024-09-29)
- BindingDB_CHEBI_ID.txt ( Mapping of BindingDB monomer (compound) IDs to CHEBI IDs. 72.08 KB, updated 2024-09-29)
- BindingDB_DrugBankID.txt ( Mapping of BindingDB monomer (compound) IDs to DrugBank IDs. 0 Bytes, updated 2024-09-29)
- BindingDB_PubMed.txt ( Collection of PubMed IDs in BindingDB. 363.05 KB, updated 2024-09-28)
- BindingDB_UniProt.txt ( Mapping of BindingDB polymer (single protein) IDs to UniProt IDs. 464.84 KB, updated 2024-09-29)
Validation sets
- BindingDBValidationSets-1.zip ( 8.08 MB, updated 2021-06-01 )
BindingDB_JChem3D.sdf (7-50 heavy atoms generated by JChem molconvert -3:S{fine}[mmff94][timelimit]{6000}[E])
- BindingDB_JChem3D.sdf.zip ( 404.63 MB, updated 2024-08-13 )
Docked Complexes
- surflex.tar ( 8.61 GB, updated 2022-03-30 )
KNIME Workflows
The BindingDB team has developed KNIME workflows for easy retrieval of BindingDB data, and for predictions of protein targets. KNIME is a graphical workbench for processing and retrieving data. The open integration platform provides over 1000 modules (nodes), including those of the KNIME community and its extensive partner network. The main advantage of retrieving data this way is flexibility; you can process the data further by adding your own nodes, and you can save the data to local disk in the format of choice. To use, simply import this workflow into the KNIME desktop, available here. In either workflow path, open the first node by double-clicking, and enter your query. Then click .Run.; the output will be collected in the final node. The workflow can be downloaded from here:BindingDB_workflows.knwf ( 188.97 KB, updated 2021-02-13 with KNIME v 4.3.1).
In order for the workflows to run properly, the following KNIME extensions need to be installed:
- KNIME & Extensions
- KNIME Community Contributions - Cheminformatics
- KNIME Labs Extensions
- Marvin Chemistry Extensions

*_2D.sdf: compound structures provided with 2-dimensional coordinates
*_3D.sdf: compound structures provided with 3-dimensional coordinates computed with Vconf (-m prep)
* _terse_: Each Compound appears once, with multiple Target data for it in the data blocks