PDBe Get Bound Molecules
Get all bound molecules (ligands, cofactors, drugs) in a PDB structure from the PDBe Graph API. Returns each bound molecule group with its chemical component ID (e.g., HEM for heme, ATP for adenosine triphosphate, REA for retinoic acid), chain location, and entity information. Essential for identifying what small molecules co-crystallized with a protein. Use this to discover ligands in a structure before analyzing binding sites. Example: 4HHB returns 6 bound molecules (4 HEM groups + 2 PO4 grou…
Overview
Get all bound molecules (ligands, cofactors, drugs) in a PDB structure from the PDBe Graph API. Returns each bound molecule group with its chemical component ID (e.g., HEM for heme, ATP for adenosine triphosphate, REA for retinoic acid), chain location, and entity information. Essential for identifying what small molecules co-crystallized with a protein. Use this to discover ligands in a structure before analyzing binding sites. Example: 4HHB returns 6 bound molecules (4 HEM groups + 2 PO4 groups); 1CBS returns REA (retinoic acid).
Status
The most recent probe succeeded. Safe to call from the agent today.
- Last probed
- 1d ago
- Last success
- 1d ago
- Last latency
- 107ms
Schema
JSON Schema the agent (or your API call) must match.
{
"properties": {
"pdb_id": {
"description": "PDB identifier (4-character code, case-insensitive). Examples: '4hhb' (hemoglobin with heme), '1cbs' (CRABP2 with retinoic acid), '6lu7' (SARS-CoV-2 Mpro with inhibitor), '3hyd' (kinase with ATP analog).",
"type": "string"
}
},
"required": [
"pdb_id"
],
"type": "object"
}Examples (1)
Default PDBe Get Bound Molecules call
{
"pdb_id": "1AKI"
}Anonymous-safe example. Rate-limited; no sign-in required.
Identifiers
- Catalog ID
- tu_PDBe_get_bound_molecules
- Tool name
- PDBe_get_bound_molecules
- Added
- 2026-04-30 22:47Z
- Tags
- tooluniverse