drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/database-lookup/references/bindingdb.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
BindingDB REST API		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/bindingdb.md	9c9bd2e9	2026-06-26	prompt	accepted	upstream	false

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	Description
/rest/getLigandsByUniprot	Ligands for a single protein target
/rest/getLigandsByUniprots	Ligands for multiple protein targets
/rest/getLigandsByPDBs	Ligands by PDB structure IDs
/rest/getTargetByCompound	Targets for a compound (SMILES similarity)

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