Fig. 2: Structure of SARS-CoV-2 PLpro in complex with inhibitor YL1004. | Nature Communications

Fig. 2: Structure of SARS-CoV-2 PLpro in complex with inhibitor YL1004.

From: YL1004 is a SARS-CoV-2 papain-like protease inhibitor with immunomodulatory and antiviral activity in mice

Fig. 2: Structure of SARS-CoV-2 PLpro in complex with inhibitor YL1004.

a Chemical structure of YL1004. b, Cartoon view of SARS-CoV-2 PLpro, color-coded by domain: Ubl domain (green), thumb domain (yellow), palm domain (pink), and finger domain (purple). The zinc ion is shown as a sphere (wheat). The N and C termini of PLpro are labeled. c, YL1004 interacts with the BL2 loop. YL1004 is represented as a violet stick model, and the 2Fo - Fc density map (gray mesh, σ = 1.5) is shown. d, Interactions between YL1004 and PLpro. Hydrogen bonds are displayed as black dashed lines. e-g, Comparative analysis of YL1004 and GRL0617 (PDB code: 7JRN) binding modes. Superimposed structures of PLpro (white)-YL1004 (violet) and PLpro-GRL0617 (blue). The hydrogen bonds of GRL0617 are displayed as yellow dashed lines. The structural displacement of the naphthyl ring is shown (arrow). Figure b-g were generated using PyMOL (http://www.pymol.org).

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