9M2V | pdb_00009m2v

Crystal Structure of the SARS-CoV-2 (COVID-19) main protease with inhibitor MC12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.250 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.206 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structure-activity relationship studies of thiazole-based derivatives leading to the identification of novel and potent SARS-CoV-2 main protease inhibitors.

Yin, W.Kong, W.P.Leung, S.L.Hung, C.H.Wong, K.Y.

(2025) Eur J Med Chem 297: 117952-117952

  • DOI: https://doi.org/10.1016/j.ejmech.2025.117952
  • Primary Citation Related Structures: 
    9M2V

  • PubMed Abstract: 

    The COVID-19 pandemic has highlighted the need for effective antiviral agents targeting SARS-CoV-2. This study presents the development of thiazole-based inhibitors against SARS-CoV-2 Main Protease, a key enzyme for viral replication. Using Masitinib and MAC-5576 as leads, we designed 29 compounds featuring a pyridinyl ester for covalent binding to Cys145 and a thiazole core for S2 subsite interaction. Structure-activity relationship (SAR) analysis identified the pyridinyl ester as a critical pharmacophore, with the thiazole core providing superior inhibition compared to oxazole. Compound MC12 (IC 50  = 77.7 ± 14.1 nM) demonstrated inhibitory activities comparable to Nirmatrelvir (IC 50  = 58.4 ± 8.6 nM). Mass spectrometry and X-ray crystallography confirmed reversible covalent binding of MC compounds to SARS-CoV-2 Main Protease. These compounds also showed low cytotoxicity and dual inhibition of SARS-CoV and SARS-CoV-2 M pro . Thiazole-based compounds thus emerge as promising leads for developing potent and safe SARS-CoV-2 M pro inhibitors.


  • Organizational Affiliation
    • State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China.

Macromolecule Content 

  • Total Structure Weight: 34.52 kDa 
  • Atom Count: 2,528 
  • Modeled Residue Count: 302 
  • Deposited Residue Count: 310 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5310Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
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
A1L8G
(Subject of Investigation/LOI)

Query on A1L8G



Download:Ideal Coordinates CCD File
B [auth A][2-[methyl(phenyl)amino]-1,3-thiazol-4-yl]methanol
C11 H12 N2 O S
ZDTJXRHMIPGVKX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.250 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.206 (DCC) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.5α = 90
b = 81.33β = 97.314
c = 88.864γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentHong Kong--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release