7D6H

Crystal structure of the SARS-CoV-2 papain-like protease (PLPro) C112S mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Development of potent and selective inhibitors targeting the papain-like protease of SARS-CoV-2.

Shan, H.Liu, J.Shen, J.Dai, J.Xu, G.Lu, K.Han, C.Wang, Y.Xu, X.Tong, Y.Xiang, H.Ai, Z.Zhuang, G.Hu, J.Zhang, Z.Li, Y.Pan, L.Tan, L.

(2021) Cell Chem Biol 28: 855-865.e9

  • DOI: https://doi.org/10.1016/j.chembiol.2021.04.020
  • Primary Citation of Related Structures:  
    7D6H, 7E35

  • PubMed Abstract: 

    The COVID-19 pandemic has been disastrous to society and effective drugs are urgently needed. The papain-like protease domain (PLpro) of SARS-CoV-2 (SCoV2) is indispensable for viral replication and represents a putative target for pharmacological intervention. In this work, we describe the development of a potent and selective SCoV2 PLpro inhibitor, 19. The inhibitor not only effectively blocks substrate cleavage and immunosuppressive function imparted by PLpro, but also markedly mitigates SCoV2 replication in human cells, with a submicromolar IC 50 . We further present a convenient and sensitive activity probe, 7, and complementary assays to readily evaluate SCoV2 PLpro inhibitors in vitro or in cells. In addition, we disclose the co-crystal structure of SCoV2 PLpro in complex with a prototype inhibitor, which illuminates their detailed binding mode. Overall, these findings provide promising leads and important tools for drug discovery aiming to target SCoV2 PLpro.


  • Organizational Affiliation

    Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Papain-like protease320Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
EC: 3.4.19.12
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC1 
Go to UniProtKB:  P0DTC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.801α = 90
b = 82.801β = 90
c = 134.408γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21822705
National Natural Science Foundation of China (NSFC)China21621002

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2021-05-19
    Changes: Database references
  • Version 1.2: 2021-05-26
    Changes: Database references
  • Version 1.3: 2021-06-30
    Changes: Database references
  • Version 1.4: 2023-11-29
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-09-18
    Changes: Derived calculations