Fig. 4
From: A new generation Mpro inhibitor with potent activity against SARS-CoV-2 Omicron variants
Crystal structure of SARS-CoV-2 Omicron variant Mpro in complex with SY110. a The chemical structure of SY110. The warhead carbon is marked with a black asterisk. b Close-up view of SY110 with the substrate-binding pocket of Mpro. SY110 is in orange, Mpro is aquamarine, His41 of Mpro blue, Cys145 yellow. Four sites S1′, S1, S2, and S4 of Mpro, and four moieties P1′, P1, P2, and P3 of SY110 are labeled, respectively. Fo – Fc density map of SY110 is shown (gray mesh, σ = 2.5). c Interactions between Mpro and SY110. The residues of Mpro involved in SY110 binding are displayed by sticks. The hydrogen bonds are displayed as red dashed lines. d Comparison of the binding modes of SY110 (orange, PDB ID: 8HHU), 11a (blue, PDB ID: 6LZE), MI-23 (wheat, PDB ID: 7D3I) and Nirmatrelvir (green, PDB ID: 7RFW). e Comparison of the binding modes between Mpro-SY110 and Mpro-calpain inhibitor XII (white, PDB: 6XFN). Images b–e were prepared using PyMOL (https://pymol.org)
