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.
might be same as pdb.ligand, not sure though
pdb-ccd
Local identifiers in Chemical Component Dictionary should match this
regular expression:
^\w{1,3}$
Compact URIs (CURIEs) constructed from Chemical Component Dictionary should match
this regular expression:
^pdb-ccd:\w{1,3}$
A summary of the relations in the Bioregistry schema can be found here.
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.
The metaregistry provides mappings between the Bioregistry and other registries. There are 5 mappings to external registries for this resource with 3 unique external prefixes.
Registry Name | Registry Metaprefix | External Prefix | Curate |
---|---|---|---|
BioContext | biocontext |
PDB-CCD
|
|
Identifiers.org | miriam |
pdb-ccd
|
|
N2T | n2t |
pdb-ccd
|
|
Prefix Commons | prefixcommons |
ccd
|
|
TogoID | togoid |
PdbCcd
|
Providers are various services that resolve CURIEs to URLs. The example CURIE
pdb-ccd:AB0
is used to demonstrate the provides available for
this resource. Generation of OLS and BioPortal URLs requires additional programmatic
logic beyond string formatting.
Name | Metaprefix | URI |
---|---|---|
Chemical Component Dictionary | pdb-ccd |
https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/AB0 |
Bioregistry | bioregistry |
https://bioregistry.io/pdb-ccd:AB0 |
Identifiers.org | miriam |
https://identifiers.org/pdb-ccd:AB0 |
Name-to-Thing | n2t |
https://n2t.net/pdb-ccd:AB0 |
Additional providers curated in the Bioregistry are listed here.
Code | Name | URL |
---|---|---|
bio2rdf |
Bio2RDF | http://bio2rdf.org/ccd:AB0 |