Ligand searching in Protein Data Bank (PDB)

Partial string search

Ligand name searching supports partial string matches. For example, searching for ‘benz’ will return all structures that contain benzene as well as those containing benzamidine.

Exact match search

For an exact match, the complete name of the ligand must be entered. Ligand searches can also be performed using the three-character ligand ID in the PDB file (the “HET” record). For example, searching for ‘HEM’ returns all structures that have a heme ligand.

MarvinSketch search

The PDB can be searched for structures containing the same ligand by drawing a ligand in MarvinSketch (provided by ChemAxon)

SMILES string search

SMILES (Simplified Molecular Input Line Entry Specification) is a comprehensive nomenclature system for chemicals.

eg.SMILES string for benzene:C1=CC=CC=C1 or c1ccccc1

SMILES search feature is the ability to query for ligands using a SMILES string representation

Go to PDB Ligand search