Fig. 2.
Docking of lead compounds to the naphthalene inhibitor binding pocket and PLpro and blind docking. Lead compounds were docked to the naphthalene inhibitor binding pocket of PLpro using the QPLD protocol of Glide, and interactions with residues are depicted. Blind docking was performed using AutoDock Vina to produce 9 poses, which are shown for the respective compounds. Residue interactions are shown as dashed lines, including hydrogen bonds (yellow), salt bridges (magenta), π−π interactions (cyan), and π−cation interactions (green). Amino acid residues are coloured according to their properties, namely hydrophobic residues (green), polar uncharged residues (cyan), negatively charged residues (red), and glycine residues (grey). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)