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. 2015 Oct 20;11(10):e1005165. doi: 10.1371/journal.ppat.1005165

Fig 4. Molecular docking of GPP3 and NLD into the VP1 pocket.

Fig 4

Both ligands are shown as sticks. (A) Overlay of the docked ligand GPP3 (cyan) by QMPLD and the experimentally determined conformation of GPP3 (magenta) (RMSD between the experimentally observed pose and docked pose for all inhibitor atoms 0.5Å) (B) NLD hydrogen-bonds with main chain nitrogen of Gln202 (RMSD between the experimentally observed pose and docked pose for all inhibitor atoms 0.6Å). (C) Highest score docking pose of protonated form of NLD hydrogen-bonds with main chain nitrogen of Gln202 (RMSD between the experimentally observed pose and docked pose for all inhibitor atoms 0.4Å). (D) Second highest docking score of NLD, note hydrogen bonds with the side chain of Asp112.