The co-crystal structure of SARS-CoV 3C Like Protease with aldehyde inhibitor M7

Experimental Data Snapshot

  • Resolution: 2.24 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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This is version 1.2 of the entry. See complete history


Comprehensive Insights into the Catalytic Mechanism of Middle East Respiratory Syndrome 3C-Like Protease and Severe Acute Respiratory Syndrome 3C-Like Protease.

Wang, H.He, S.Deng, W.Zhang, Y.Li, G.Sun, J.Zhao, W.Guo, Y.Yin, Z.Li, D.Shang, L.

(2020) ACS Catal 10: 5871-5890

  • DOI: https://doi.org/10.1021/acscatal.0c00110
  • Primary Citation of Related Structures:  
    6LNQ, 6LNY, 6LO0

  • PubMed Abstract: 

    Coronavirus 3C-like protease (3CL Pro ) is a highly conserved cysteine protease employing a catalytic dyad for its functions. 3CL Pro is essential to the viral life cycle and, therefore, is an attractive target for developing antiviral agents. However, the detailed catalytic mechanism of coronavirus 3CL Pro remains largely unknown. We took an integrated approach of employing X-ray crystallography, mutational studies, enzyme kinetics study, and inhibitors to gain insights into the mechanism. Such experimental work is supplemented by computational studies, including the prereaction state analysis, the ab initio calculation of the critical catalytic step, and the molecular dynamic simulation of the wild-type and mutant enzymes. Taken together, such studies allowed us to identify a residue pair (Glu-His) and a conserved His as critical for binding; a conserved GSCGS motif as important for the start of catalysis, a partial negative charge cluster (PNCC) formed by Arg-Tyr-Asp as essential for catalysis, and a conserved water molecule mediating the remote interaction between PNCC and catalytic dyad. The data collected and our insights into the detailed mechanism have allowed us to achieve a good understanding of the difference in catalytic efficiency between 3CL Pro from SARS and MERS, conduct mutational studies to improve the catalytic activity by 8-fold, optimize existing inhibitors to improve the potency by 4-fold, and identify a potential allosteric site for inhibitor design. All such results reinforce each other to support the overall catalytic mechanism proposed herein.

  • Organizational Affiliation

    State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and KLMDASR of Tianjin, Nankai University, No. 38 Tongyan Road, Haihe Education Park, Tianjin 300350, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Severe Acute Respiratory Syndrome Coronavirus 3c Like Protease306Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus)
Explore P0C6X7 
Go to UniProtKB:  P0C6X7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6X7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EJF (Subject of Investigation/LOI)
Query on EJF

Download Ideal Coordinates CCD File 
B [auth A]N-[(2S)-3-methyl-1-[[(2S)-4-methyl-1-oxidanylidene-1-[[(2S)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]pentan-2-yl]amino]-1-oxidanylidene-butan-2-yl]-1H-indole-2-carboxamide
C27 H37 N5 O5
Experimental Data & Validation

Experimental Data

  • Resolution: 2.24 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.068α = 90
b = 80.529β = 104.36
c = 53.354γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21672115

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Advisory, Derived calculations
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description