7TUU

Structure of the SARS-CoV-2 main protease in complex with halicin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Repurposing Halicin as a potent covalent inhibitor for the SARS-CoV-2 main protease.

Yang, K.S.Alex Kuo, S.T.Blankenship, L.R.Geng, Z.Z.Li, S.G.Russell, D.H.Yan, X.Xu, S.Liu, W.R.

(2022) Curr Res Chem Biol 2: 100025-100025

  • DOI: https://doi.org/10.1016/j.crchbi.2022.100025
  • Primary Citation of Related Structures:  
    7TUU

  • PubMed Abstract: 

    The rapid spread of COVID-19 has caused a worldwide public health crisis. For prompt and effective development of antivirals for SARS-CoV-2, the pathogen of COVID-19, drug repurposing has been broadly conducted by targeting the main protease (M Pro ), a key enzyme responsible for the replication of virus inside the host. In this study, we evaluate the inhibition potency of a nitrothiazole-containing drug, halicin, and reveal its reaction and interaction mechanism with M Pro . The in vitro potency test shows that halicin inhibits the activity of M Pro an IC 50 of 181.7 ​nM. Native mass spectrometry and X-ray crystallography studies clearly indicate that the nitrothiazole fragment of halicin covalently binds to the catalytic cysteine C145 of M Pro . Interaction and conformational changes inside the active site of M Pro suggest a favorable nucleophilic aromatic substitution reaction mechanism between M Pro C145 and halicin, explaining the high inhibition potency of halicin towards M Pro .


  • Organizational Affiliation

    Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.


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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.213α = 90
b = 84.362β = 95.608
c = 90.093γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PROTEUM PLUSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Welch FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description