FIGURE 9.

The substrate-binding cleft located between domains I and II of Mpro. (A) The active site cavity is located on the surface of Mpro. Subsites S1, S2, and S4 are shaped into well-formed binding pockets. The catalytic dyad is highlighted in red with the residues that flank the cavity. The oxyanion hole created by residues 140–144 is highlighted. (B) A close-up view of the catalytic site cavity in which the catalytic residues (Cys145 and His41) are highlighted in red. The catalytic water molecule is shown as a red sphere. Hydrogen bonds are shown as black dashed lines.