Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) Covalently Bound to Compound C7

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

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Design, synthesis and in vitro evaluation of novel SARS-CoV-2 3CL pro covalent inhibitors.

Stille, J.K.Tjutrins, J.Wang, G.Venegas, F.A.Hennecker, C.Rueda, A.M.Sharon, I.Blaine, N.Miron, C.E.Pinus, S.Labarre, A.Plescia, J.Burai Patrascu, M.Zhang, X.Wahba, A.S.Vlaho, D.Huot, M.J.Schmeing, T.M.Mittermaier, A.K.Moitessier, N.

(2021) Eur J Med Chem 229: 114046-114046

  • DOI: https://doi.org/10.1016/j.ejmech.2021.114046
  • Primary Citation of Related Structures:  
    7MLF, 7MLG

  • PubMed Abstract: 

    Severe diseases such as the ongoing COVID-19 pandemic, as well as the previous SARS and MERS outbreaks, are the result of coronavirus infections and have demonstrated the urgent need for antiviral drugs to combat these deadly viruses. Due to its essential role in viral replication and function, 3CL pro (main coronaviruses cysteine-protease) has been identified as a promising target for the development of antiviral drugs. Previously reported SARS-CoV 3CL pro non-covalent inhibitors were used as a starting point for the development of covalent inhibitors of SARS-CoV-2 3CL pro . We report herein our efforts in the design and synthesis of submicromolar covalent inhibitors when the enzymatic activity of the viral protease was used as a screening platform.

  • Organizational Affiliation

    Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase304Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: (PDB Primary Data), (UniProt), 3.4.22 (UniProt), (UniProt), (UniProt), (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), (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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C7A (Subject of Investigation/LOI)
Query on C7A

Download Ideal Coordinates CCD File 
B [auth A]N-(4-tert-butylphenyl)-2-chloro-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]acetamide
C25 H32 Cl N3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.81α = 90
b = 53.54β = 98.92
c = 45.33γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
DIALSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2022-01-19
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description