The PDB Chemical Component Dictionary (formerly the HET Group Dictionary) is available in PDB and mmCIF formats, and is updated weekly. Any comments and suggestions are greatly appreciated.
This section provides descriptions and examples of the contents of the PDB format and mmCIF format Chemical Component Dictionaries as well as a description of the contents of an entry in Ligand Depot.
Ligand Depot1 has been created as a data warehouse which integrates databases, services, tools and methods related to small molecules bound to macromolecules. It was created to help users explore the PDB Chemical Component Dictionary and the small molecule contents of the PDB.
In particular it allows users to:
Search for PDB ligands by chemical name or formula
Search for PDB ligands by 3-letter ID ( e.g. Thr yields results for Threonine )
Find a PDB ligand by structure or substructure
Both the PDB format and mmCIF format Chemical Component Dictionaries contain a listing describing all of the standard and non-standard residues present in the PDB archive. The overall format of the dictionaries is an alphabetical concatenation of all available groups.
Non-standard residues are identified in the PDB format files as HET groups and in mmCIF format files as chemical components. Residues such as prosthetic groups, inhibitors, solvent molecules, and ions for which coordinates are supplied are considered to be non-standard if they are:
not one of the standard amino acids, and
not one of the nucleic acids (C, G, A, T, U, and I), and
an unknown amino acid or nucleic acid where UNK is used to indicate the unknown residue name.
Each chemical component is assigned an ID code of not more than three alphanumeric characters.
Each time a new chemical component is created, it is entered into both the PDB format and mmCIF format dictionaries. A new group is not released in the public version of the dictionary until the entry containing it is released.
1Z Feng, L Chen, H Maddula, O Akcan, HM Berman, J Westbrook, ACA Program and Abstract Book Series 2 Vol 30 ISSN 0569-4221, Northern Kentucky Convention Center, July 26-31, 2003.
Dictionary Record Format
Example: Acetic Acid
Dictionary Record Format
Example: Acetic Acid