Fig. 6.
Binding mode and molecular interaction of compounds with PLpro. (A) Ribbon representation of PLpro (PDB: 6w9c) showing the binding mode of docked GRL0617 (Pettersen et al., 2004), withanolide A (Liu et al., 2020), isocodonocarpine (blue) and calonysterone (orange). The active site and catalytic triad Cys112-His273-Asp287 is shown in red sticks. (B) The superimposition of binding mode of docked GRL0617 (Pettersen et al., 2004) to SRAR-CoV-2 (cyan) (PDB: 6w9c) with the binding mode of co-crystalized GRL0617 (yellow) in complex with SARS-CoV (gold) (PDB: 3E9S). (a). 2D ligand–protein interaction of (b) withanolide A (c) isocodonocarpine and (d) calonysterone with PLpro.