During an audit of our PDB ligand links in http://www.guidetopharmacology.org/ we have been looking at intersects between PDBe ligands (via UniChem) and PubChem CIDs for what should be the same structures in NCBI MMDB. While the comparison is preliminary, from our total of ~ 900 (curated real lead-like structures) we see peculiar discordance of well over 100 in both directions (i.e. PDBe with no exact match in MMDB and visa versa). We have seen this issue before for indivdual cases but I wonder if anyone has done a systematic comparison (e.g. via InChIKeys) ?. The numbers dont add up for starters with 19713 in PDBe and 27973 for MMDB.
Some boil down to just two hydrogens but still a missmatch (e.g. AWJ)
Others are more serious such as 35Q