PDB to InChI Converter
If you need a canonical, database-friendly identifier for a ligand in a crystal structure, InChI is the target format.
Why InChI rather than SMILES
PDB files vary in how atoms and bonds are recorded. InChI normalises the result, so two structures of the same ligand from different entries produce the same identifier — which is exactly what you need for cross-referencing against PubChem or ChEMBL.
Working with the whole file
A full PDB includes protein, water and ions. Converting the entire file yields an InChI that
tries to describe everything at once. For ligand-level identifiers, first extract the
HETATM records of the molecule you care about.
Reliability
Crystal structures often lack hydrogens and may contain alternate conformations. The resulting InChI is a best-effort interpretation — verify against the deposited chemical component dictionary when precision matters.