9KSI | pdb_00009ksi

Crystal Structure of SARS-CoV-2 main protease in complex with compound 5

• PDB DOI: https://doi.org/10.2210/pdb9KSI/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-29 Released: 2025-04-02 
• Deposition Author(s): Zhong, Y., Zhao, L., Zhang, W., Peng, W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.243 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Expanding the utilization of binding pockets proves to be effective for noncovalent small molecule inhibitors against SARS-CoV-2 M pro.

Yang, Q., Huang, X., Zhang, H., Sun, J., Tang, J., Chen, Z., Liu, L., Liu, M., Sun, Z., Tang, Z., Wei, D., Wang, D., Wang, Y., Yan, M., Zhao, L., Zhu, A., Zhong, Y., Yang, H., Zhao, Y., Dai, J., Shi, Y., Huang, B., Zhang, W., Zhao, J., Chen, X., Rao, Z., Peng, W.

(2025) Eur J Med Chem 289: 117497-117497

• PubMed: 40090296 
• DOI: https://doi.org/10.1016/j.ejmech.2025.117497
• Primary Citation of Related Structures:  
  9KR5, 9KSH, 9KSI, 9KSJ, 9KSK


• PubMed Abstract: 
  

  The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in millions of deaths and continues to pose serious threats to global public health. The main protease (M ^pro ) of SARS-CoV-2 is crucial for viral replication and its conservation, making it an attractive drug target. Here, we employed a structure-based drug design strategy to develop and optimize novel inhibitors targeting SARS-CoV-2 M ^pro . By fully exploring occupation of the S1, S2, and S3/S4 binding pockets, we identified eight promising inhibitors with half-maximal inhibitory concentration (IC ₅₀ ) values below 20 nM. The cocrystal structure of M ^pro with compound 10 highlighted the crucial roles of the interactions within the S3/S4 pockets in inhibitor potency enhancement. These findings demonstrated that expanding the utilization of these binding pockets was an effective strategy for developing noncovalent small molecule inhibitors that target SARS-CoV-2 M ^pro . Compound 4 demonstrated outstanding in vitro antiviral activity against wild-type SARS-CoV-2 with an EC ₅₀ of 9.4 nM. Moreover, oral treatment with compounds 1 and 9 exhibited excellent antiviral potency and substantially ameliorated virus-induced tissue damage in the lungs of Omicron BA.5-infected K18-human ACE2 (K18-hACE2) transgenic mice, indicating that these novel noncovalent inhibitors could be potential oral agents for the treatment of COVID-19.

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Organizational Affiliation: 
• State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 511436, China; Guangzhou National Laboratory, Guangzhou, 510005, China.
Guangzhou National Laboratory, Guangzhou, 510005, China; Innovative Center for Pathogen Research, Guangzhou National Laboratory, Guangzhou, 510005, China.
Beijing StoneWise Technology Co. Ltd., Beijing, 100080, China.
State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 511436, China; The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 511436, China.
Guangzhou National Laboratory, Guangzhou, 510005, China; Innovative Center for Pathogen Research, Guangzhou National Laboratory, Guangzhou, 510005, China; Guangzhou Medical University, Guangzhou, 511436, China.
Guangzhou National Laboratory, Guangzhou, 510005, China; Innovative Center for Pathogen Research, Guangzhou National Laboratory, Guangzhou, 510005, China; The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 511436, China.
State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 511436, China; Guangzhou National Laboratory, Guangzhou, 510005, China; The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 511436, China.
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, 518112, China.
Technology Centre, Guangzhou Customs, Guangzhou, 510623, China.
Beijing StoneWise Technology Co. Ltd., Beijing, 100080, China. Electronic address: [e-mail].
State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 511436, China; Guangzhou National Laboratory, Guangzhou, 510005, China; Innovative Center for Pathogen Research, Guangzhou National Laboratory, Guangzhou, 510005, China. Electronic address: [e-mail].
State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 511436, China; Guangzhou National Laboratory, Guangzhou, 510005, China; The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 511436, China. Electronic address: [e-mail].
State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 511436, China; Guangzhou National Laboratory, Guangzhou, 510005, China; The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 511436, China. Electronic address: [e-mail].
Guangzhou National Laboratory, Guangzhou, 510005, China; Innovative Center for Pathogen Research, Guangzhou National Laboratory, Guangzhou, 510005, China; Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084, China; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. Electronic address: [e-mail].
State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 511436, China; Guangzhou National Laboratory, Guangzhou, 510005, China; Innovative Center for Pathogen Research, Guangzhou National Laboratory, Guangzhou, 510005, China; The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 511436, China; University of South China, Hengyang, 421001, China. Electronic address: [e-mail].

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)

Biological Assembly Evidence: fluorescence resonance energy transfer

Macromolecule Content 

• Total Structure Weight: 34.35 kDa 
• Atom Count: 2,434 
• Modeled Residue Count: 305 
• Deposited Residue Count: 305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	305	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EGP (Subject of Investigation/LOI)	B [auth A]	(6E)-1-[[5-chloranyl-4-fluoranyl-2-(4-fluoranylphenoxy)phenyl]methyl]-6-(6-chloranyl-2-methyl-indazol-5-yl)imino-3-(5-methoxypyridin-3-yl)-1,3,5-triazinane-2,4-dione C30 H21 Cl2 F2 N7 O4 SUQMPBJCRZMCTG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.243 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.125	α = 90
b = 83.678	β = 115.8
c = 51.794	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
PHENIX	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Zhong, Y., Zhao, L., Zhang, W., Peng, W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32100142
Other private		2023A04J0163
Other private		SRPG22-003
Other private		SRPG22-011

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release