7RNW

SARS-CoV-2 Main Protease in complex with a cyclic peptide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Antiviral cyclic peptides targeting the main protease of SARS-CoV-2.

Johansen-Leete, J.Ullrich, S.Fry, S.E.Frkic, R.Bedding, M.J.Aggarwal, A.Ashhurst, A.S.Ekanayake, K.B.Mahawaththa, M.C.Sasi, V.M.Luedtke, S.Ford, D.J.O'Donoghue, A.J.Passioura, T.Larance, M.Otting, G.Turville, S.Jackson, C.J.Nitsche, C.Payne, R.J.

(2022) Chem Sci 13: 3826-3836

  • DOI: https://doi.org/10.1039/d1sc06750h
  • Primary Citation of Related Structures:  
    7RNW

  • PubMed Abstract: 

    Antivirals that specifically target SARS-CoV-2 are needed to control the COVID-19 pandemic. The main protease (M pro ) is essential for SARS-CoV-2 replication and is an attractive target for antiviral development. Here we report the use of the Random nonstandard Peptide Integrated Discovery (RaPID) mRNA display on a chemically cross-linked SARS-CoV-2 M pro dimer, which yielded several high-affinity thioether-linked cyclic peptide inhibitors of the protease. Structural analysis of M pro complexed with a selenoether analogue of the highest-affinity peptide revealed key binding interactions, including glutamine and leucine residues in sites S1 and S2, respectively, and a binding epitope straddling both protein chains in the physiological dimer. Several of these M pro peptide inhibitors possessed antiviral activity against SARS-CoV-2 in vitro with EC 50 values in the low micromolar range. These cyclic peptides serve as a foundation for the development of much needed antivirals that specifically target SARS-CoV-2.


  • Organizational Affiliation

    School of Chemistry, The University of Sydney Sydney NSW 2006 Australia richard.payne@sydney.edu.au.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B, C, D
306Severe 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-DTY-LEU-GLN-TYR-ALA-VAL-LEU-ARG-HIS-LYS-ARG-ARG-GLU-SECE [auth X],
F [auth Y],
G [auth Z],
H [auth W]
15synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.36α = 90
b = 201.726β = 113.49
c = 60.543γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaCE200100012

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2022-05-04
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description