UniChem Database

Overview

UniChem is a chemical structure cross-referencing service from EMBL-EBI that links compound records across 20+ public chemistry databases using InChI-based identifiers. It maps a single chemical entity to its corresponding IDs in ChEMBL, DrugBank, PubChem, ChEBI, PDB (RCSB and PDBe), SureChEMBL, HMDB, DrugCentral, BindingDB, and others. Access is via a free REST API at https://www.ebi.ac.uk/unichem/api/v1/ - no API key required. Important: every cross-reference query is sent as POST with a JSON body; only the catalogue endpoint GET /sources is implemented as a GET.

When to Use

• Translating a ChEMBL compound ID to a PubChem CID, DrugBank accession, or ChEBI ID for cross-database analysis
• Resolving an InChIKey to all database sources where a compound appears
• Finding all structurally related compounds (same connectivity, different stereochemistry/salts) across databases using connectivity search
• Validating compound identity across sources before merging datasets from multiple databases
• Building a compound cross-reference table for a drug discovery project (linking bioactivity data in ChEMBL to structural data in PDB)
• Checking if a synthesized compound or a vendor compound exists in any public database by InChIKey
• For full bioactivity profiles (IC50, Ki) use chembl-database-bioactivity; UniChem provides only ID cross-references, not experimental data
• For compound property prediction or substructure searching use pubchem-compound-search; UniChem is for identifier translation only