Bringing clarity to chemistry at PDBe

New chemistry images at PDBe
01 November 2018

The PDB is an archive of macromolecular structures, but the small molecules bound in these structures are the focus of much interest. We have recently made some changes to the way we display images of small molecules at PDBe, which brings a lot more clarity to their chemistry.

In addition to tens of thousands of different macromolecules in the PDB archive, there are also over 25,000 unique small molecules. These are all defined in the chemical component dictionary (CCD) and include a diverse range of compounds including drugs, sugars, enzymatic cofactors and inorganic metal-containing complexes. In many cases, the molecular structure can be quite complex and difficult to represent in a 2D image. We have recently made improvements to the processes we use to create 2D molecular structure images to ensure that we can show more accurate chemical diagrams and provide users with a more helpful representation of the molecule.

Ligand 7MT: representation with old (top) and new (bottom) PDBe chemistry images

Old (top) and new (bottom) 2D images for the terbium complex "Crystallophore n°1", ligand 7MT.

Previously, there were a number of small molecules which were missing images, either because of the complexity of the chemistry, or due to missing idealised coordinates. Our new process is now able to generate ideal coordinates for most molecules where they are missing in the reference CCD files. The use of templates in the image generation process has ensured better depiction of molecules with complex chemistry too; 98.5% of images now have no atom collisions.

These changes should ensure that PDBe users will be presented with a much clearer view of these small, but very important, molecules.