Cortexa research tool·structure·bindingdb

BindingDB Get Ligands By PDB

Get binding affinity data for proteins by PDB structure ID. Returns ligands with measured affinities for the protein structure. Useful for structure-activity relationship analysis when you have co-crystal structures.

Livelast probed 2026-04-30 23:07Z· 111msCortexa

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed: 1d ago
Last success: 1d ago
Last latency: 111ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "affinity_cutoff": {
      "default": 10000,
      "description": "Maximum affinity in nM (default: 10000)",
      "type": "integer"
    },
    "pdb_ids": {
      "description": "Comma-separated PDB IDs (e.g., 1Q0L,3ANM)",
      "type": "string"
    },
    "sequence_identity": {
      "default": 100,
      "description": "Minimum sequence identity % (default: 100)",
      "type": "integer"
    }
  },
  "required": [
    "pdb_ids"
  ],
  "type": "object"
}

Examples (1)

Default BindingDB Get Ligands By PDB call

public-safeinput

{
  "affinity_cutoff": 1,
  "pdb_ids": "1AKI",
  "sequence_identity": 1
}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_BindingDB_get_ligands_by_pdb
Tool name: BindingDB_get_ligands_by_pdb
Added: 2026-04-30 22:47Z
Tags: tooluniverse

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