wwPDB News - PDB Entries with Novel Ligands Now Distributed Only in PDBx/mmCIF and PDBML File Formats

wwPDB News logo

The PDB three-character Chemical Component IDs are consumed and PDB has begun issuing five-character alphanumeric accession codes for CCD IDs in the OneDep system. To avoid confusion with current four-character PDB IDs, four-character codes are not used. Owing to limitations of the legacy PDB file format, PDB entries containing the new five character ID codes are distributed in PDBx/mmCIF and PDBML formats and will not be supported by the legacy PDB file format ().

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 is asking users and software developers to review their code and remove any current limitations on PDB and CCD ID lengths, and to enable use of PDBx/mmCIF format files.  to assist with code revisions.

To learn about PDBx/mmCIF, please visit .

For any further information please contact us at [email protected]