9KGN | pdb_00009kgn

Discovery of an orally bioavailable reversible covalent SARS-CoV-2 Mpro inhibitor with pan-coronavirus activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.226 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Discovery of an Orally Bioavailable Reversible Covalent SARS-CoV-2 M pro Inhibitor with Pan-Coronavirus Activity.

Tan, Q.W.Vankadara, S.Fong, J.Y.See, Y.Y.Baburajendran, N.Ng, P.S.Xu, W.Yeo, Y.K.Wang, W.Low, C.H.Tan, L.H.Ju Tay, E.G.Wong, Y.X.Huang, C.Sim, S.Ang, S.H.Min Toh, H.H.Mohammad, J.Wang, G.Liu, B.Tan, S.T.Kwek, P.Z.Dawson, M.D.Oh, Q.Y.Koh, X.Joy, J.Lee, M.A.Stunkel, W.Pendharkar, V.Hentze, H.Lim, S.P.Ethirajulu, K.Brian Chia, C.S.Cherian, J.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00581
  • Primary Citation of Related Structures:  
    9KGJ, 9KGN, 9KGQ, 9KGR, 9KGS

  • PubMed Abstract: 

    Resulting in several million deaths globally, the COVID-19 pandemic has highlighted the criticality of antiviral drugs during a viral pandemic. Herein, we describe our efforts toward targeting SARS-CoV-2 M pro , a key viral protease, which led to the discovery of compound 18 , a reversible covalent inhibitor with potent antiviral activity against several clinical variants of SARS-CoV-2. Compound 18 demonstrated dose-dependent efficacy in a mouse-adapted SARS-CoV-2 infection model, with favorable pharmacokinetic profiles in mice, rats, dogs, and monkeys.


  • Organizational Affiliation

    Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos #05-01, Singapore 138670, Republic of Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5A [auth B],
B [auth A]
311Severe 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

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
compound 3
C, D
4synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.226 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.461α = 90
b = 98.659β = 108.933
c = 59.735γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release