BindingDB REST API

Base URLs

https://bindingdb.org/rest/
https://bindingdb.org/axis2/services/BDBService/

Auth

No API key required. Fully open and free.

Response Format

Default is XML. Append &response=application/json to any endpoint for JSON.

Key Endpoints

Endpoint Details

Get ligands for a single target

GET https://bindingdb.org/rest/getLigandsByUniprot?uniprot={UNIPROT_ID};{IC50_cutoff_nM}&response=application/json

• uniprot — UniProt ID followed by ; and affinity cutoff in nM
• Returns monomerIDs, SMILES, affinity types (IC50, Ki, Kd), and values
• Returns empty string if UniProt ID not found

Example:

https://bindingdb.org/rest/getLigandsByUniprot?uniprot=P35355;100&response=application/json

Get ligands for multiple targets

GET https://bindingdb.org/rest/getLigandsByUniprots?uniprot={IDs}&cutoff={nM}&response=application/json

• uniprot — Comma-separated UniProt IDs
• cutoff — Affinity cutoff in nM
• Returns empty string if no matching IDs

Example:

https://bindingdb.org/rest/getLigandsByUniprots?uniprot=P00176,P00183&cutoff=10000&response=application/json

Get ligands by PDB structure

GET https://bindingdb.org/rest/getLigandsByPDBs?pdb={PDBs}&cutoff={nM}&identity={percent}&response=application/json

• pdb — Comma-separated PDB IDs
• cutoff — Affinity cutoff in nM
• identity — Sequence identity cutoff (percent, e.g. 92)

Example:

https://bindingdb.org/rest/getLigandsByPDBs?pdb=1Q0L,3ANM&cutoff=100&identity=92&response=application/json

Find targets for a compound (similarity search)

GET https://bindingdb.org/rest/getTargetByCompound?smiles={SMILES}&cutoff={similarity}&response=application/json

• smiles — Compound SMILES (must be URL-encoded)
• cutoff — Tanimoto similarity cutoff (decimal, e.g. 0.85)
• Returns similar compounds with their protein targets and affinities

Example:

https://bindingdb.org/rest/getTargetByCompound?smiles=CCC%5BN%2B%5D%28C%29%28C%29CCn1nncc1COc1cc%28%3DO%29n%28C%29c2ccccc12&cutoff=0.85&response=application/json

Rate Limits

No documented limit. Keep requests to ~1 per second as a courtesy.

Notes

• The API surface is small (4 endpoints) but focused on binding affinity data
• For compound-name search, resolve to SMILES first via PubChem, then use getTargetByCompound
• For bulk data access, use downloadable TSV/SDF files from https://www.bindingdb.org/bind/chemsearch/marvin/Download.jsp
• Contains ~3.2M binding measurements for ~1.4M compounds and ~11.4K targets