1.9. Protein Data Bank (PDB): a key source for protein-bound ligand structures

        The Protein Data Bank (PDB) is an archive of the experimentally determined 3-D structures of large biological molecules such as proteins and nucleic acids. These structures were determined primarily by using X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy.  While PDB is not a small molecule database, it contains the 3-D structures of many proteins with small-molecule ligands bound to them.  PDB allows users to search for proteins that an input small molecule binds to.  Considering that it is not possible to experimentally determine how small molecules (such as drug or toxic chemicals) actually bind to their target proteins in a living organism, PDB is the most widely used resource for experimentally determined protein-bound structures of small molecules.  The PDB are maintained by the Worldwide PDB (wwPDB)³³, and freely accessible via the websites of its member organizations: PDBe (PDB in Europe)^34,35, PDBj (PDB Japan)^36,37, RCSB PDB (Research Collaboratory for Structural Bioinformatics PDB)^38,39.