MCP server exposing 3 tools for bindingdb.
This URL is a JSON-RPC 2.0 endpoint over HTTP. Issue POST requests with a JSON-RPC body. Browsers and search crawlers land here on GET.
POST https://gateway.pipeworx.io/bindingdb/mcp
Content-Type: application/json
{"jsonrpc":"2.0","id":1,"method":"tools/list"}bindingdb_ligands_by_uniprot — Measured binding affinities (Ki, Kd, IC50, EC50 in nM) for every ligand BindingDB has curated against a UniProt target, each with the PubMed ID of the paper it was measured in. AUTHORITATIVE for "what compounds bind this protein and how tightly" — this is experimental medicinal-chemistry data, not a prediction or a web summary. Pass one or more UniProt accessions (e.g. P24941 for CDK2).bindingdb_targets_by_smiles — Given a compound SMILES, the protein targets BindingDB has measured it (or a structurally similar compound) against, with species and affinity. AUTHORITATIVE for compound-to-target and off-target lookups grounded in published measurements. Use a similarity cutoff below 1.0 to pull analogues as well as the exact structure.bindingdb_by_pdb — Measured binding affinities for the ligands associated with a PDB structure entry, linking a solved co-crystal to the potency numbers published for that target. AUTHORITATIVE for "what is the measured affinity of the ligand in this PDB structure". Takes a single 4-character PDB ID (e.g. 3EML).Code samples (curl / TypeScript / one-click client install), schemas, and the live playground are on the pack page:
https://pipeworx.io/packs/bindingdb/
Pipeworx is an open MCP gateway connecting AI agents to live data. pipeworx.io