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The Chemical Component Dictionary has been remediated to address the inconsistencies in older dictionary entries that resulted in valence problems, missing model coordinates, and redundant ligands.
In this new dictionary, the nomenclature has been standardized:
A summary of the new dictionary content is provided.
A companion dictionary of amino acid variants provides additional nomenclature information for the protonation states of standard amino acids in N-terminal, C-terminal, and free forms. This dictionary also includes common side chain protonation states.
A summary page for each chemical component provides a 2D chemical diagram and 3D graphic (using Jmol) of an existing ligand followed by a structure report containing information on the physical and chemical features of the ligand is available. The report will also include status information regarding when the ligand was first created and the last modification date. The end of the report will have links to the component definition in CIF and PDBML/XML formats along with model coordinates, idealized coordinates, and chemical diagrams.
Components may be searched using their assigned 3-letter component identifier. For example, the small molecule heme has the component ID "HEM", whereas caffeine has the component ID "CFF". Please note that the assignment of component 3-letter identifiers is arbitrary and may not reflect the actual compound name or synonym in any way. For example, the PDB ID for tris-hydroxymethyl-methyl- ammonium is "144". It is also important to note that the 3-letter PDB ID may consist of 1 to 3 letters (e.g. "C" for cytidine-5'-monophosphate, "PT" for platinum).
Browse by ID: The indices below can be used to browse the dictionary based upon their assigned 3-letter component identifier:
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