8ZT9 | pdb_00008zt9

The Crystal structure of mol066 bound to the main protease (3CLpro/Mpro) of SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb8ZT9/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-06 Released: 2025-06-11 
• Deposition Author(s): Yan, M., Zhang, H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.186 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Development of pyrimidone derivatives as nonpeptidic and noncovalent 3-chymotrypsin-like protease (3CL pro ) inhibitors with anti-coronavirus activities.

Pan, F., Zhou, Q., Yan, M., Yang, S., Hu, R., Chen, Y., Wen, Y., Chao, Y., Xie, C., Ou, W., Li, Y., Zhang, H., Guo, D., Zhang, X.

(2025) Bioorg Chem 154: 107988-107988

• PubMed: 39591689 
• DOI: https://doi.org/10.1016/j.bioorg.2024.107988
• Primary Citation Related Structures: 
  8ZT9, 8ZUB, 8ZUC


• PubMed Abstract: 
  

  3CL ^Pro is crucial to the life cycle of SARS-CoV-2 and exhibits high sequence similarity with other coronaviruses, while being absent in human proteases. This makes it an ideal target for developing broad-spectrum antiviral drugs. Ensitrelvir (S-217622) is the only launched non-covalent, non-peptidomimetic 3CL ^Pro inhibitor, offering certain advantages in terms of dosage and metabolism. Using S-217622 as the lead, we designed and synthesized 43 pyrimidone derivatives and conducted a systematic evaluation of their structure-activity relationships. Among them, A36 exhibited strong inhibitory activity against several β-coronaviruses and demonstrated low cytotoxicity. A36 also displayed moderate stability in mouse liver microsomes. Co-crystal structure analysis of 3CL ^Pro in complex with A36 revealed the similar binding mode with S-217622. A36 shows strong potential as a promising lead for broad-spectrum anti-coronavirus therapy, warranting further investigation.

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Organizational Affiliation: 
• Shenzhen Key Laboratory of Small Molecule Drug Discovery and Synthesis, Department of Chemistry, Shenzhen Grubbs Institute and Medi-X Pingshan, Southern University of Science and Technology, Shenzhen 518000, China.
Shenzhen Key Laboratory of Small Molecule Drug Discovery and Synthesis, Department of Chemistry, Shenzhen Grubbs Institute and Medi-X Pingshan, Southern University of Science and Technology, Shenzhen 518000, China. Electronic address: [e-mail].
Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518000, China.
Guangzhou National Laboratory, Guangzhou, Guangdong Province 510005, China.
State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510180, China.
Institute of High Energy Physics, CAS, Beijing 100000, China; China Spallation Neutron Source, CAS, Dongguan, Guangdong 523000, China. Electronic address: [e-mail].
Guangzhou National Laboratory, Guangzhou, Guangdong Province 510005, China. Electronic address: [e-mail].
Shenzhen Key Laboratory of Small Molecule Drug Discovery and Synthesis, Department of Chemistry, Shenzhen Grubbs Institute and Medi-X Pingshan, Southern University of Science and Technology, Shenzhen 518000, 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: gel filtration

Macromolecule Content 

• Total Structure Weight: 68 kDa 
• Atom Count: 5,268 
• Modeled Residue Count: 604 
• Deposited Residue Count: 604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	302	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D87 (Subject of Investigation/LOI)	C [auth A], D [auth B]	6-[(6-chloranyl-2-propan-2-yl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]pyrimidine-2,4-dione C25 H22 Cl F3 N8 O2 JGYXSDVCSGOBIX-UHFFFAOYSA-N
GOL	E [auth B], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.186 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.475	α = 90
b = 99.384	β = 108.15
c = 58.793	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Yan, M., Zhang, H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release