HMDB Database

Overview

The Human Metabolome Database (HMDB) is a comprehensive, freely available resource containing detailed information about small molecule metabolites found in the human body.

When to Use This Skill

This skill should be used when performing metabolomics research, clinical chemistry, biomarker discovery, or metabolite identification tasks.

Database Contents

HMDB version 5.0 (current as of 2025) contains:

• 220,945 metabolite entries covering both water-soluble and lipid-soluble compounds
• 8,610 protein sequences for enzymes and transporters involved in metabolism
• 130+ data fields per metabolite including:
  • Chemical properties (structure, formula, molecular weight, InChI, SMILES)
  • Clinical data (biomarker associations, diseases, normal/abnormal concentrations)
  • Biological information (pathways, reactions, locations)
  • Spectroscopic data (NMR, MS, MS-MS spectra)
  • External database links (KEGG, PubChem, MetaCyc, ChEBI, PDB, UniProt, GenBank)

Core Capabilities

1. Web-Based Metabolite Searches

Access HMDB through the web interface at https://www.hmdb.ca/ for:

Text Searches:

• Search by metabolite name, synonym, or identifier (HMDB ID)
• Example HMDB IDs: HMDB0000001, HMDB0001234
• Search by disease associations or pathway involvement
• Query by biological specimen type (urine, serum, CSF, saliva, feces, sweat)

Structure-Based Searches:

• Use ChemQuery for structure and substructure searches
• Search by molecular weight or molecular weight range
• Use SMILES or InChI strings to find compounds

Spectral Searches:

• LC-MS spectral matching