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

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