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PDB-CCD
Reference dictionary defining all residues and small molecule components observed in Protein Data Bank structures.
What PDB-CCD is
The Chemical Component Dictionary (PDB-CCD), maintained by the Worldwide Protein Data Bank (wwPDB) and formerly known as the HET Group Dictionary, is the external reference dictionary defining every residue and small molecule component found in PDB entries.
Prior to the dictionary's establishment, chemical information in the PDB archive was stored primarily as basic connection tables in the legacy PDB HET dictionary. PDB-CCD provides comprehensive chemical descriptions that capture systematic nomenclature, stereochemical assignments, chemical formulae, formal charges, formula weights, and both experimental and idealised coordinates.
The dictionary serves as the chemical foundation for macromolecular structure entries across the archive. New definitions are added alongside each weekly PDB release, and existing entries are routinely reviewed and remediated to ensure consistency.
How it is organised
Each component is indexed by a unique three-character alphanumeric identifier. The definitions are structured using mmCIF categories: chem_comp supplies high-level chemical descriptors and metadata; chem_comp_atom and chem_comp_bond detail individual atoms, formal charges, aromaticity, leaving-atom flags, and bond orders; and pdbx_chem_comp_descriptor and pdbx_chem_comp_identifier record software-generated chemical descriptors and registry numbers.
Idealised three-dimensional coordinates are computationally generated using Corina, or OpenEye's OMEGA if coordinate generation issues occur, alongside heavy-atom model coordinates extracted directly from specific PDB entries. Chemical descriptors such as SMILES, InChI, and InChIKey are generated using CACTVS and OpenEye. The resource is supplemented by a companion protonation variant dictionary defining standard amino acid ionization states, as well as a model data file mapping components to Cambridge Structural Database (CSD) records with corresponding R-values and crystallographic metrics.
Key facts
- Curator
- Worldwide Protein Data Bank (wwPDB)
- Record count
- 50.1k components
- Component identifier
- 3-character alphanumeric code
- Idealised coordinate generators
- Molecular Networks' Corina and OpenEye's OMEGA
- Available formats
- mmCIF, SDF/MOL, tab-delimited text, legacy PDB HET
- Update frequency
- Weekly
What you can use it for
- Ligand identity and topology retrieval
- Inspect systematic names, connectivity, aromaticity, leaving atoms, and stereochemistry for any small molecule, non-standard residue, or solvent found in a PDB entry.
- Chemical similarity and substructure searching
- Search PDB ligands and components matching or closely resembling specific molecular formulae, substructures, or SMILES and InChI descriptors using RCSB PDB Chemical Search or PDBeChem.
- Amino acid protonation state reference
- Look up standardized atom nomenclature and definitions for common side-chain, free, N-terminal, and C-terminal protonation forms using the companion protonation variant dictionary.
- Crystallographic ligand cross-referencing
- Map PDB chemical components to small-molecule crystal structures in the Cambridge Structural Database (CSD) via the Chemical Component Model data file.
Strengths and limits
Good at
- Provides standardized stereochemistry, connectivity, and chemical descriptors for every residue and ligand observed across the PDB archive.
- Supplies both observed experimental Cartesian coordinates from macromolecular models and calculated idealised 3D coordinates.
- Maintains historical integrity by keeping obsoleted components marked with an OBS status tag rather than deleting them.
Watch out for
- Primary component definitions are restricted by the historical three-character alphanumeric identifier limit.
- Extended identifier codes used in the protonation variant companion dictionary cannot appear directly in standard three-character PDB coordinate files.
- Complete dictionary download files are large and can require substantial download time.
Questions
Can I search PDB-CCD without writing code?
PDB-CCD is catalogued here but not yet queried live, so the agent can point you to it but cannot search it for you yet.
Can I reuse data from PDB-CCD?
PDB-CCD publishes its own terms of use; read them on https://www.wwpdb.org/data/ccd before reusing its records.
What molecule types are covered by the dictionary?
It describes standard and modified amino acids, standard and modified nucleotides, small molecule ligands, and solvent molecules observed in PDB archive structures.
How are the idealised coordinates calculated?
Idealised coordinates are generated computationally using Molecular Networks' Corina software, falling back to OpenEye's OMEGA if geometry calculation issues occur.
What happens when an entry in the dictionary is replaced or obsoleted?
Obsoleted entries remain in the dictionary flagged with release status OBS, and records indicate the replacement component identifier where applicable.
How can researchers search the dictionary interactively?
The dictionary can be browsed and searched using PDBeChem and RCSB PDB Chemical Search, which support 3-letter code queries, substructure searches, formula ranges, and chemical descriptor comparisons.
How to cite it
J.D. Westbrook, C. Shao, Z. Feng, M. Zhuravleva, S. Velankar, J. Young (2014) The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank Bioinformatics doi: 10.1093/bioinformatics/btu789
Written from PDB-CCD's own website and reference material. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.