`ligand`

Pack: rcsb-pdb · Connect: https://pipeworx.io/mcp (see Connect below for a single-pack URL)

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

“Ligand / cofactor / drug bound to [pdb_id]” / “small molecule in [PDB entry]” — fetch a non-polymer ligand record (small molecule, cofactor, ion, or bound drug) for a PDB entry. Use to inspect what’s bound in a co-crystal structure — common in drug discovery / SBDD.

Parameters

Name	Type	Required	Description
`pdb_id`	string	yes
`ligand_id`	string	yes

Example call

Arguments

{
  "pdb_id": "1abc",
  "ligand_id": "ATP"
}

curl

curl -X POST https://gateway.pipeworx.io/rcsb-pdb/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"ligand","arguments":{"pdb_id":"1abc","ligand_id":"ATP"}}}'

TypeScript (@pipeworx/sdk)

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

const result = await pipeworx.call('ligand', {
  "pdb_id": "1abc",
  "ligand_id": "ATP"
});

Response shape

Full JSON Schema

{
  "type": "object",
  "description": "Non-polymer ligand record (cofactor, drug, etc.)"
}

Connect

Add this to your MCP client config — every tool in the catalog, including this one — or use one-click install buttons:

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

Connect to just the rcsb-pdb pack

{
  "mcpServers": {
    "rcsb-pdb": {
      "url": "https://gateway.pipeworx.io/rcsb-pdb/mcp"
    }
  }
}

See Getting Started for client-specific install steps.

ligand