The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It 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, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names.

Comment

might be same as pdb.ligand, not sure though

Prefix

pdb-ccd

Alternative Prefixes

pdbechem PDBeChem

Keywords

chemical classification compound

License

http://www.ebi.ac.uk/Information/termsofuse.html

Links

Homepage

Publications

2003 Announcing the worldwide Protein Data Bank

Pattern for Local Unique Identifiers

Local identifiers in Chemical Component Dictionary should match this regular expression:
^\w{1,3}$

Example Local Unique Identifiers

AB0   Resolve
A   Resolve
PI   Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from Chemical Component Dictionary should match this regular expression:
^pdb-ccd:\w{1,3}$

Example CURIEs

pdb-ccd:AB0
pdb-ccd:A
pdb-ccd:PI

Contact

Helen Berman   0000-0002-3337-0660

Contributors

contributor Birgit Meldal   0000-0003-4062-6158   bmeldal-eg

A summary of the relations in the Bioregistry schema can be found here.

Has URI collision with (bioregistry.schema:0000016 )

This resource shares one or more URI format strings with pdb.ligand .

Therefore, when generating an extended prefix map, pdb-ccd, its CURIE prefix synonyms, and its URI prefix synonyms are merged into the record for pdb.ligand . If you believe that these are two distinct semantic spaces and should not be merged, please open a new issue on the Bioregistry issue tracker for discussion.

In Collection (2)

ChEBI Data Sources Synapse.org external links

Mappings from records in Bioregistry to external registries comprises the metaregistry. This resource has 5 mappings to external registries with 3 unique external prefixes.

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier AB0 is used to demonstrate the providers available for Chemical Component Dictionary. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.

Additional providers curated in the Bioregistry are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.