Bindingdb

liveBiologyChemistry

BindingDB — measured protein/small-molecule binding affinities.

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free tier50 calls/day

Tools

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

No parameters required.

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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 look

No parameters required.

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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

No parameters required.

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Test with curl

The gateway speaks JSON-RPC 2.0 over HTTP POST. You can test any pack directly from the terminal.

List available tools
bash
curl -X POST https://gateway.pipeworx.io/bindingdb/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/list"}'
Call a tool
bash
curl -X POST https://gateway.pipeworx.io/bindingdb/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"bindingdb_ligands_by_uniprot","arguments":{}}}'

Use with the SDK

Install @pipeworx/sdk to call tools from any TypeScript/Node project.

TypeScript
import { Pipeworx } from '@pipeworx/sdk';
const px = new Pipeworx();
const result = await px.call("bindingdb_ligands_by_uniprot", {});
ask_pipeworx
// Or ask in plain English:
const answer = await px.ask("bindingdb — measured protein/small-molecule binding affinities");