What is PDBeChem?

PDBe provides a range of services for exploring the binding of small molecules such as drugs, co-factors, co-enzymes, prosthetic groups and biomacromolecules.

One such service is PDBeChem (PDBe-KB Ligand pages), which stores information regarding all chemical species (small molecules, ligands, metal ions, amino acids and nucleotides) found in the Protein Data Bank (PDB) archive.

Small molecules are dealt with in the PDB archive as formally equivalent to macromolecular residues. Each one is given a unique code but these are often arbitrary and so you can’t necessarily guess what the compound might be from the code.

This mini-tutorial uses PDBeChem to explore compounds in the PDB archive that are chemically similar to the benzothiophene derivatives bound to Christmas Factor in PDB entries 3lc3 and 3lc5. You can find out more about Christmas Factor in the accompanying Quips article.

The search methods it shows should be of general use to you as you explore small molecules in PDB structures.