[3dem] Coming Soon: PDB Entries with Novel Ligands Distributed Only in PDBx/mmCIF and PDBML File Formats

[Justin Flatt]

At current growth rates, we anticipate running out of three-character 
Chemical Component IDs by the end of 2023. After this point, the wwPDB 
will issue five-character alphanumeric accession codes for CCD IDs in 
the OneDep system. To avoid confusion with current four-character PDB 
IDs, four-character codes will not be used. Owing to limitations of the 
legacy PDB file format, PDB entries containing the new five character ID 
codes will only be distributed in PDBx/mmCIF and PDBML formats (see 
previous announcement [1]).

In addition, wwPDB has reserved a set of CCD IDs: 01 - 99, DRG, INH, LIG 
that will never be used in the PDB. These reserved codes can be used for 
new ligands during structure determination so that they can be 
identified as new upon deposition and added to the CCD during 
biocuration.

wwPDB asks users and software developers to review code to remove any 
current limitations on CCD ID lengths, and to enable use of PDBx/mmCIF 
format files. Example files with extended CCD IDs are available via 
GitHub [2] to assist code revisions. Information about the PDBx/mmCIF 
dictionary and file format is provided at mmcif.wwpdb.org [3].

For any further information please contact us at info at wwpdb.org.

Links:
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[1] https://urldefense.com/v3/__http://www.wwpdb.org/news/news?year=2023*63ff72ccc031758bf1c30ff7__;Iw!!Mih3wA!BMXihq7zM1PCcHAQxDWcebMdn-i6YMD4ihZXYAMaFHxUqj2FDMnr4rzJQ425YPbfp0w1VgCl2LJuZ9Ldd2yjdwnh$ 
[2] https://urldefense.com/v3/__https://github.com/wwPDB/extended-wwPDB-identifier-examples__;!!Mih3wA!BMXihq7zM1PCcHAQxDWcebMdn-i6YMD4ihZXYAMaFHxUqj2FDMnr4rzJQ425YPbfp0w1VgCl2LJuZ9Ldd5H7JLNo$ 
[3] https://urldefense.com/v3/__https://mmcif.wwpdb.org/__;!!Mih3wA!BMXihq7zM1PCcHAQxDWcebMdn-i6YMD4ihZXYAMaFHxUqj2FDMnr4rzJQ425YPbfp0w1VgCl2LJuZ9Ldd8Vpc-SE$ 
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