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. 2022 Jul 8;12:11585. doi: 10.1038/s41598-022-15181-y

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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SARS-CoV-2 PL^pro principal component analysis. (A) Distributions over the two significant PCs (PC1 and PC2) separated for each simulated system apostructure (PDB: 7lbr) is highlighted in grey; GRL-0617 bound structures (GLR067-7JIR) in sky-blue; PLP_Synder530 bound structures (PLP_Synder530 - 7JIW) in magenta, XR8-89 bound structures (XR8-89 - 7LBR) in orange and CPD7 bound structures (CPD7) in dark brown. (B) Extreme motions from the PC1 displayed over the PL^pro tertiary structure represented by arrows. (C) Extreme motions from the PC2 displayed over the PL^pro tertiary structure represented by arrows. (D) Ubl-Catalytic connection path, with relevant residues highlighted as sticks (E) Distance values between C111 to H272 along with the simulations depicting the full extension of the inhibitor binding site opening. (F) S2 binding site opening representation, and (G) S2 vector angle analysis describing the opening/closing of this region. For E and G, ligands are coloured according to figure legend.