# get-binding-site

`station__rcsb-org__get-binding-site` · external (needs EXECUTION_BACKEND_URL configured) · domain `rcsb-org` · pv-relevance `pv-adjacent`

Compute the binding pocket for a ligand in a PDB entry: all protein residues with any atom within a distance cutoff (default 5 Å) of any ligand atom. Use to highlight the binding pocket in the 3D scene and to annotate key contact residues for mechanism explanations.

> **Note:** This tool routes through an external execution backend. If `EXECUTION_BACKEND_URL` is unset on the server, calls return JSON-RPC error `-32603 "Tool execution backend not configured"`. Tools with `backend: native` execute in-process and are always callable.

## Agent metadata

- `idempotent`: unknown
- `read_only`: unknown
- `expected_latency_ms`: unknown (not yet contract-tested)
- `cost_tokens_estimate`: unknown

## Input schema

- `pdb_id` *string* (required) — 4-character PDB identifier
- `ligand_code` *string* (required) — 3-letter chem component ID of the ligand in the structure (e.g., 'CFF')
- `cutoff_angstrom` *number* — Distance cutoff in Ångströms (default 5.0, max 10.0)

## Example call

```json
POST /api/mcp
Content-Type: application/json

{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "station__rcsb-org__get-binding-site",
    "arguments": {
      "pdb_id": "",
      "ligand_code": ""
    }
  }
}
```

## Related

- [/tools](/tools) — all 3062 tools
- [/tools/rcsb-org__get-binding-site](/tools/rcsb-org__get-binding-site) — HTML page
- [/tools/rcsb-org__get-binding-site/json](/tools/rcsb-org__get-binding-site/json) — JSON form (agent-friendly)
- [/api/mcp](/api/mcp) — endpoint
- [/AGENTS.md](/AGENTS.md) — agent guide