bindingdb_by_pdb

Pack: bindingdb · Endpoint: https://gateway.pipeworx.io/bindingdb/mcp

No MCP client? Call it directly: GET https://gateway.pipeworx.io/v1/tools/bindingdb_by_pdb for the schema, then POST the same URL with its arguments for the data.

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).

Parameters

NameTypeRequiredDescription
pdbstringyesPDB entry ID, 4 characters (e.g. “3EML”)
limitnumbernoMax rows to return, 1-500 (default 50)

Example call

Arguments

{
  "pdb": "3EML",
  "limit": 3
}

curl

curl -X POST https://gateway.pipeworx.io/bindingdb/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"bindingdb_by_pdb","arguments":{"pdb":"3EML","limit":3}}}'

TypeScript (@pipeworx/sdk)

import { Pipeworx } from '@pipeworx/sdk';
const pipeworx = new Pipeworx();

const result = await pipeworx.call('bindingdb_by_pdb', {
  "pdb": "3EML",
  "limit": 3
});

Connect

Add this to your MCP client config, or use one-click install buttons:

{
  "mcpServers": {
    "bindingdb": {
      "url": "https://gateway.pipeworx.io/bindingdb/mcp"
    }
  }
}

See Getting Started for client-specific install steps.

Regenerated from source · build September 18, 2026