Fig. 4: Ligands binding to SARS-CoV-2 PLpro.
From: Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors
A Compound 1 binding to PLpro. B Compound 2 binding to PLpro. C Compound 3 binding to PLpro. D Model of compound 4 (yellow sticks) binding to PLpro. Ligands are shown as green sticks and PLpro is in magenta. Dashed lines show hydrogen bonds, water molecules are shown as blue spheres. In A–C the 2Fo − mFc electron density maps are shown as a grey mesh, contoured at 1.2 σ. E Compound 2 (green sticks) binds to a groove on the surface of PLpro protein (surface of palm subdomain is in white and thumb subdomain is in light blue) with the active site catalytic triad surface is shown in red in the end of a slender tunnel. Peptide LRGG from ubiquitin structure in complex with SARS PLpro (PDB id: 4MOW) is shown in yellow and peptide positions corresponding P1–P4 sites are marked in white.
