8JPQ

SARS-CoV-2 Mpro in complex with D-5-96


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

The S1'-S3' Pocket of the SARS-CoV-2 Main Protease Is Critical for Substrate Selectivity and Can Be Targeted with Covalent Inhibitors.

Liu, M.Li, J.Liu, W.Yang, Y.Zhang, M.Ye, Y.Zhu, W.Zhou, C.Zhai, H.Xu, Z.Zhang, G.Huang, H.

(2023) Angew Chem Int Ed Engl 62: e202309657-e202309657

  • DOI: https://doi.org/10.1002/anie.202309657
  • Primary Citation of Related Structures:  
    8GW4, 8GWS, 8JPQ

  • PubMed Abstract: 

    The main protease (M pro ) of SARS-CoV-2 is a well-characterized target for antiviral drug discovery. To date, most antiviral drug discovery efforts have focused on the S4-S1' pocket of M pro ; however, it is still unclear whether the S1'-S3' pocket per se can serve as a new site for drug discovery. In this study, the S1'-S3' pocket of M pro was found to differentially recognize viral peptidyl substrates. For instance, S3' in M pro strongly favors Phe or Trp, and S1' favors Ala. The peptidyl inhibitor D-4-77, which possesses an α-bromoacetamide warhead, was discovered to be a promising inhibitor of M pro , with an IC 50 of 0.95 μM and an antiviral EC 50 of 0.49 μM. The M pro /inhibitor co-crystal structure confirmed the binding mode of the inhibitor to the S1'-S3' pocket and revealed a covalent mechanism. In addition, D-4-77 functions as an immune protectant and suppresses SARS-CoV-2 M pro -induced antagonism of the host NF-κB innate immune response. These findings indicate that the S1'-S3' pocket of SARS-CoV-2 M pro is druggable, and that inhibiting SARS-CoV-2 M pro can simultaneously protect human innate immunity and inhibit virion assembly.


  • Organizational Affiliation

    State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5302Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ACE-ALA-ILE-V3E4synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
V3E
Query on V3E
B
L-PEPTIDE LINKINGC10 H13 N O3PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.508α = 90
b = 53.876β = 101.3
c = 114.113γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-23
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Database references
  • Version 2.0: 2024-10-02
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 3.0: 2024-11-20
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Structure summary