Figure 2
From: Structural analysis of the coronavirus main protease for the design of pan-variant inhibitors
Imaginary shape of Mpro binding pocket. (a) The graphical blueprint of the active site boundary of imaginary ligands to SARS-CoV-2 Mpro. The mapping in mesh representation shows nitrogen atoms as blue mesh, oxygen atoms as red mesh, and carbon atoms as grey mesh. Paxlovid’s Nirmatrelvir (PF-07321332) with ligand’s code: 4WI (PDB:7vh8 in protomer A) is in stick representation with its carbon atoms in lemon colour. The mesh on the left-hand panel shows nitrogen at position N5 (blue), from 4WI exists at the location where the majority of the data from large datasets suggested that this location should be oxygen (red mesh harbouring N5 of 4WI, top right). This oxygen can interact with nitrogen from the main chain of Gly143. Nirmatrelvir (PF-07321332) occupies most of the space but there are still areas that more atoms can be added (gray mesh represents carbon atom location from the ligands which are found surrounding PF-07321332, lemon sticks). (b) The interacting residues, i.e. Thr25 and Cys44 (highlighted in red, rotated 20°), Asn142 (highlighted in yellow, rotated 65°), and Gln192 (highlighted in magenta, rotated 70°), locates in a close proximity to the SARS-CoV-2 Mpro-specific ligand atoms of the active site boundary (beige mesh blobs). Cyan mesh blob identifies the binding boundary of SARS-CoV Mpro. The figure was created by using PyMOL Version 2.5.3 (https://pymol.org)25.
