Fig. 8.
Crystallographic structure of the SARS-CoV-2 3CLpro bound to the N-(pyridin-3-ylmethyl)thioformamide moiety (in pink) from the compound 1 (PDB ID: 7NTQ) (a). The 2Fo-Fc electron-density map, contoured at 1.5 σ, is shown as light grey mesh. (b) Interaction of the ligand (cpd 1 after Cys145 binding) with the 3CLpro S1 pocket. The analysis of the interaction was made using LigPlot+ (v2.2.4). 3CLpro and ligand bonds are shown in brown and purple, respectively. Water molecules are displayed as cyan spheres. Dashed green lines and dashed red lines represent hydrogen bonds and hydrophobic interactions, respectively. The 3CLpro residues that are involved in hydrogen bonds have their name displayed in green whereas the residues making hydrophobic contact(s) are indicated with their name surrounded by red spikes. Atoms involved in hydrophobic contact(s) are surrounded by red spikes.