Fig. 2.

Ligand binding and characteristics of the predicted M^pro allosteric site in SARS-CoV-2 and HCoV-OC43. (A) Scatter plot of selected allosteric site ligands and their respective binding energies in SARS-CoV-2 (orange) and HCoV-OC43 (blue). (B) Kernel density plots of the ligand RMSD values for the last 10 ns of the 100 ns MD simulations. (C) Protein-ligand interactions for the six compounds in SARS-CoV-2. Residue contributions from protomer A and B are labelled in black and red respectively. (D) Sequence alignment of M^pro from the two strains, showing residue conservation (highlighted in light brown) with additional functional annotations. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)