9KGN | pdb_00009kgn

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

• PDB DOI: https://doi.org/10.2210/pdb9KGN/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-08 Released: 2025-08-20 
• Deposition Author(s): Baburajendran, N.
• Funding Organization(s): Not funded

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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

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 68: 17087-17102

• PubMed: 40773370 
• DOI: https://doi.org/10.1021/acs.jmedchem.5c00581
• Primary Citation 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.

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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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 69.26 kDa 
• Atom Count: 4,950 
• Modeled Residue Count: 609 
• Deposited Residue Count: 630 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A [auth B], B [auth A]	311	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
compound 3	C, D	4	synthetic construct	Mutation(s): 0

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 = 55.461	α = 90
b = 98.659	β = 108.933
c = 59.735	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Baburajendran, N.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release
  
• Version 1.1: 2025-09-10
  Changes: Database references