7MLF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 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 ...

    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. Electronic address: nicolas.moitessier@mcgill.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseA304Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C7A
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
FMBPORSTYBRWAD-HSZRJFAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

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