Interesting. One of the most helpful ways of ascertaining whether you do have a
bound ligand (or, as Jay suggests, bound but modified ligand/protein) is, of
course, to compare the electron density you see in the complex with the
corresponding unliganded (let’s say apo) complex (in your case, the
It has always struck me as something of a surprise that pre-publication review
of structures in protein-land differs so significantly from small
molecule-land. One of the activities of the CCDC is to supply pre-release CSD
structures to referees, using a simple, automated system to establish tha
I'm sad to think that scientists may not 'bother' to use the CSD system 'just'
to check the geometry of small molecule ligands, as they may, of course, be the
main focus of the study, or the focus of subsequent researchers who use the
structures. Moreover, comparison of small molecule and protei
