The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank

Bioinformatics. 2015 Apr 15;31(8):1274-8. doi: 10.1093/bioinformatics/btu789. Epub 2014 Dec 2.


The Chemical Component Dictionary (CCD) is a chemical reference data resource that describes all residue and small molecule components found in Protein Data Bank (PDB) entries. The CCD contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, chemical descriptors, systematic chemical names and idealized coordinates. The content, preparation, validation and distribution of this CCD chemical reference dataset are described.

Availability and implementation: The CCD is updated regularly in conjunction with the scheduled weekly release of new PDB structure data. The CCD and amino acid variant reference datasets are hosted in the public PDB ftp repository at,, and its mirror sites, and can be accessed from


Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Chemical*
  • Databases, Protein*
  • Dictionaries, Chemical as Topic*
  • Internet
  • Ligands
  • Macromolecular Substances / chemistry*
  • Molecular Sequence Annotation*
  • User-Computer Interface


  • Ligands
  • Macromolecular Substances