8JOP

Crystal structure of the SARS-CoV-2 main protease in complex with 11a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.200 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Discovery of benzodiazepine derivatives as a new class of covalent inhibitors of SARS-CoV-2 main protease.

Wang, F.Zeng, R.Qiao, J.Xia, A.Li, Y.Li, F.Wu, Y.Liu, Y.Zhao, X.Lei, J.Yang, S.

(2023) Bioorg Med Chem Lett 92: 129407-129407

  • DOI: https://doi.org/10.1016/j.bmcl.2023.129407
  • Primary Citation of Related Structures:  
    8JOP

  • PubMed Abstract: 

    The COVID-19 pandemic has caused people immense suffering all over the world. Although the World Health Organization (WHO) has announced the end of the pandemic, the sporadic virus epidemic is still ongoing and may exist permanently. Effective antivirals against SARS-CoV-2 are important to deal with the long-term threat. The main protease (M pro ) is a crucial target for drug development due to its role in the process of virus's replication and transcription. Herein, we report benzodiazepine derivatives as a new class of M pro inhibitors. Structure-activity relationship (SAR) studies led to the discovery of the most active compound, methyl 10-(2-chloroacetyl)-1-oxo-11-(4-(trifluoromethyl)phenyl)-2,3,4,5,10,11-hexahydro-1H-dibenzo[b,e][1,4]-diazepine-7-carboxylate (11a), which shows an IC 50 value of 0.180 ± 0.004 μM. The X-ray crystal structure shows that 11a covalently binds to M pro . Collectively, we have obtained a new small molecule inhibitor targeting M pro , which can serve as a lead compound for subsequent drug discovery against SARS-CoV-2.


  • Organizational Affiliation

    Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UWO (Subject of Investigation/LOI)
Query on UWO

Download Ideal Coordinates CCD File 
B [auth A]methyl (6~{R})-5-ethanoyl-7-oxidanylidene-6-[4-(trifluoromethyl)phenyl]-8,9,10,11-tetrahydro-6~{H}-benzo[b][1,4]benzodiazepine-2-carboxylate
C24 H21 F3 N2 O4
JYNGJASZTLERPY-JOCHJYFZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.577α = 90
b = 51.656β = 104.64
c = 43.437γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
Aimlessdata scaling
XDSdata 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)China2021YFF0702004

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary