Pdbe Compound Tools

Configuration File: pdbe_compound_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the pdbe_compound_tools.json configuration file.

Available Tools

PDBe_get_compound_structures (Type: PDBECompoundTool)

Get PDB structures containing a specific chemical compound (ligand/cofactor/ion). Returns compoun…

PDBe_get_compound_structures tool specification

Tool Information:

  • Name: PDBe_get_compound_structures

  • Type: PDBECompoundTool

  • Description: Get PDB structures containing a specific chemical compound (ligand/cofactor/ion). Returns compound details and a list of PDB entry IDs where the compound appears. Useful for finding all crystal structures with a drug or cofactor bound, studying binding site diversity, or identifying protein targets of a compound. Example: ‘ATP’ appears in thousands of PDB structures (kinases, ATPases, motor proteins); ‘HEM’ appears in hemoglobins, cytochromes, peroxidases; ‘NAG’ (N-acetylglucosamine) appears in glycoproteins.

Parameters:

  • comp_id (string) (required) PDB chemical component ID (3-letter code). Examples: ‘ATP’, ‘HEM’, ‘NAG’, ‘FAD’, ‘NAD’, ‘ZN’, ‘GOL’. Case-insensitive.

Example Usage:

query = {
    "name": "PDBe_get_compound_structures",
    "arguments": {
        "comp_id": "example_value"
    }
}
result = tu.run(query)

PDBe_get_compound_summary (Type: PDBECompoundTool)

Get detailed chemical compound information from PDBe by PDB chemical component ID (3-letter code)…

PDBe_get_compound_summary tool specification

Tool Information:

  • Name: PDBe_get_compound_summary

  • Type: PDBECompoundTool

  • Description: Get detailed chemical compound information from PDBe by PDB chemical component ID (3-letter code). Returns molecular formula, weight, formal charge, compound type, InChI identifier, InChI key, SMILES representations, systematic IUPAC names, and cross-references to PubChem, DrugBank, EPA CompTox, ClinicalTrials, and other chemical databases. Essential for studying protein-ligand interactions, drug binding, or identifying compounds in crystal structures. Example: ‘ATP’ returns adenosine-5’-triphosphate (C10H16N5O13P3, 507.18 Da, linked to DrugBank DB00171 and PubChem 5957); ‘HEM’ returns protoporphyrin IX containing Fe (616.49 Da); ‘CFF’ returns caffeine (194.19 Da).

Parameters:

  • comp_id (string) (required) PDB chemical component ID (3-letter code). Examples: ‘ATP’, ‘HEM’ (heme), ‘NAG’ (N-acetylglucosamine), ‘CFF’ (caffeine), ‘GOL’ (glycerol), ‘ZN’ (zinc ion), ‘FAD’, ‘NAD’. Case-insensitive.

Example Usage:

query = {
    "name": "PDBe_get_compound_summary",
    "arguments": {
        "comp_id": "example_value"
    }
}
result = tu.run(query)