Primary Citation PubMed: 17269759
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Multiple virtual screening approaches for finding new hepatitis C virus RNA-dependent RNA polymerase inhibitors: structure-based screens and molecular dynamics for the pursue of new poly pharmacological inhibitors.
(2012) BMC Bioinformatics 13 Suppl 17
PubMed: 23282180 | PubMedCentral: PMC3521232 | DOI: 10.1186/1471-2105-13-S17-S5
For the palm region, docking of the co-crystallized ligand resulted in a pose with a RMSD of 1.2 Å and 1.09 Å calculated from superposition of heavy atoms of the docked ligands over th... crystal coordinates for PDB coordinates 2JC1 and 3D5M respectively.
Figure 6 A) Overlay of docked and PDB coordinates of 2JC1 ligand for the Palm I site (original ligand pose coloured blue, docked ligand pose coloured pink); B) docked pose of DB05039 it shows a very good placement of the diethyl-indanyl group into the deep pocket .
The plots represent the systems of NS5B structure complexed with the original PDB ligand coordinates and docked hits coordinates (at the palm region) in the order: 2JC1, 3D5M, DB05039, DB01940, DB00560, DB04142 (left to right, top to buttom).
For each site we have identified from the PDB five publicly available crystal structures of polymerase bound to different ligands representing the different binding sites (3MWW for an indole-based inhibitor [ 43 ], 2JC1 for Acyl pyrolidine inhibitors [ 44 ], 3D5M pyridazinone inhibitor [ 45 ] and 3FRZ [ 38 ] dihydropyran inhibitor) of the non-nucleoside inhibitors, mainly targeting the thumb I, thumb II and the palm region.
The original ligand of 2JC1 (Figure 6-A ), as in the crystal structure, had a docked pose exhibiting a single hydrogen bond with the TYR448 residue, which suggests the sufficiency of that bonding - in addition to filling the deep hydrophobic pocket with the p -tert-butyl phenyl group - as a criterion for inhibition at this site.
Figure 9 RMSD across time along the production phase for the three protein ligand systems of the three PDB coordinates in the order: 2JC1 (palm), 3D5M (palm), 3FRZ (thumb II) (top to bottom) .
Publication Year: 2012
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