Dear CCP4bb, I recently solved the 2.0 Å crystal structure of a small hydrophobic molecule bound to a protein. A glutamine sidechain nitrogen is positioned ~3.3-3.4 Å from a double bond in the small molecule acyl chain. Could this be a similar interaction to the X-H (where X-H is an H-bond donor) Pi bonding seen between aromatic residues and hydrogen bond donors, i.e., is this an interaction that could be contributing to the protein-ligand binding energy?
I haven't found a precedent for X-H-Pi hydrogen bonding between amides and alkenes in the protein literature or my searches of the PDB; however, I did find several papers that consider the role of such interactions in small molecules: http://pubs.acs.org/doi/abs/10.1021/jp046031o http://pubs.acs.org/doi/pdf/10.1021/ja00288a034 http://pubs.acs.org/doi/pdf/10.1021/ja0013531 Thank you in advance for considering my question regarding this protein-ligand interaction. Any thoughts on this unusual interaction will be greatly appreciated. Sincerely, Evan Waldron Neiditch Lab Graduate Student Rutgers, NJMS
