Yes, it very well could be, the distance is pretty typical for this kind of weak, "non-cannonical" hydrogen bond. However, directionality is an important aspect of hydrogen bonding and its hard to say if this is a reasonable bond without a (small filesize so no one's inbox gets overloaded) picture of the geometry.
Matthew Merski University of Warsaw On Wed, Jun 14, 2017 at 7:23 PM, Evan Waldron <evwaldro...@gmail.com> wrote: > 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 >
