Selected article for: "binding substrate and electron density"
Author: Wenhao Dai; Bing Zhang; Xia-Ming Jiang; Haixia Su; Jian Li; Yao Zhao; Xiong Xie; Zhenming Jin; Jingjing Peng; Fengjiang Liu; Chunpu Li; You Li; Fang Bai; Haofeng Wang; Xi Cheng; Xiaobo Cen; Shulei Hu; Xiuna Yang; Jiang Wang; Xiang Liu; Gengfu Xiao; Hualiang Jiang; Zihe Rao; Leike Zhang; Yechun Xu; Haitao Yang; Hong Liu
Title: Structure-Based Design, Synthesis and Biological Evaluation of Peptidomimetic Aldehydes as a Novel Series of Antiviral Drug Candidates Targeting the SARS-CoV-2 Main Protease
  • Document date: 2020_3_28
    • ID: b4joa5tx_16
    Snippet: The electron density map clearly showed the compound 11a in the substrate binding pocket of SARS-CoV-2 M pro in an extended conformation (Figure 2A The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.25.996348 doi: bioRxiv preprint 11a at P2 enters deep into the S2 site, stacking to the imidazole ring of His41 ( Figure 2B ). The cyclohexyl group is also surrounded by the side chains of M.....
    Document: The electron density map clearly showed the compound 11a in the substrate binding pocket of SARS-CoV-2 M pro in an extended conformation (Figure 2A The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.25.996348 doi: bioRxiv preprint 11a at P2 enters deep into the S2 site, stacking to the imidazole ring of His41 ( Figure 2B ). The cyclohexyl group is also surrounded by the side chains of Met49, Tyr54, Met165 and Asp187, producing extensive hydrophobic interactions (Figure 2B) . The indole group of 11a at P3 is exposed to solvent (S4 site) and is stabilized by Glu166 through a hydrogen bond (Figure 2B) . The side chains of residues Pro168 and Gln189 interact with the indole group of 11a through hydrophobic interactions.

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