8HEF | pdb_00008hef

The Crystal structure of deuterated S-217622 (Ensitrelvir) bound to the main protease (3CLpro/Mpro) of SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb8HEF/pdb

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


• Deposited: 2022-11-08 Released: 2023-04-19 
• Deposition Author(s): Yan, M., Zhang, H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 
  0.170 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.133 (Depositor) 
• R-Value Observed: 
  0.135 (Depositor) 

Starting Model: experimental

Literature

Synthesis of deuterated S-217622 (Ensitrelvir) with antiviral activity against coronaviruses including SARS-CoV-2.

Yang, Y., Cao, L., Yan, M., Zhou, J., Yang, S., Xu, T., Huang, S., Li, K., Zhou, Q., Li, G., Zhu, Y., Cong, F., Zhang, H., Guo, D., Li, Y., Zhang, X.

(2023) Antiviral Res 213: 105586-105586

• PubMed: 36997073 
• DOI: https://doi.org/10.1016/j.antiviral.2023.105586
• Primary Citation Related Structures: 
  8HEF


• PubMed Abstract: 
  

  S-217622 (Ensitrelvir) is a reversible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 3-chymotrypsin-like protease (3CL ^pro ) inhibitor which obtained emergency regulatory approval in Japan for the treatment of SARS-CoV-2 infection on Nov 22, 2022. Herein, analogs of S-271622 with deuterium-for-hydrogen replacement were synthesized for comparison of the antiviral activities and pharmacokinetic (PK) profiles. Compared to the parent compound, C11-d2-S-217622 compound YY-278 retained in vitro activity against 3CL ^pro and SARS-CoV-2. X-ray crystal structural studies showed similar interactions of SARS-CoV-2 3CL ^pro with YY-278 and S-271622. The PK profiling revealed the relatively favorable bioavailability and plasma exposure of YY-278. In addition, YY-278, as well as S-217622, displayed broadly anti-coronaviral activities against 6 other coronaviruses that infect humans and animals. These results laid the foundation for further research on the therapeutic potential of YY-278 against COVID-19 and other coronaviral diseases.

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Organizational Affiliation: 
• Department of Chemistry, College of Science, Academy for Advanced Interdisciplinary Studies, and Medi-X Pingshan, Southern University of Science and Technology, Shenzhen, Guangdong, 518000, China.
Centre for Infection and Immunity Studies (CIIS), School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China.
Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518000, China.
Guangzhou Laboratory, Bio-island, Guangzhou, Guangdong, 510320, China.
Guangdong Province Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, Guangdong, 510663, China.
Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518000, China. Electronic address: [e-mail].
Centre for Infection and Immunity Studies (CIIS), School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China; Guangzhou Laboratory, Bio-island, Guangzhou, Guangdong, 510320, China. Electronic address: [e-mail].
Department of Chemistry, College of Science, Academy for Advanced Interdisciplinary Studies, and Medi-X Pingshan, Southern University of Science and Technology, Shenzhen, Guangdong, 518000, China. Electronic address: [e-mail].
Department of Chemistry, College of Science, Academy for Advanced Interdisciplinary Studies, and Medi-X Pingshan, Southern University of Science and Technology, Shenzhen, Guangdong, 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: 67.74 kDa 
• Atom Count: 5,360 
• Modeled Residue Count: 602 
• Deposited Residue Count: 602 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	301	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  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
7YY (Subject of Investigation/LOI)	C [auth A], E [auth B]	6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione C22 H17 Cl F3 N9 O2 QMPBBNUOBOFBFS-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free:  0.170 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.133 (Depositor) 
• R-Value Observed: 0.135 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.8	α = 90
b = 99.06	β = 108.8
c = 59.67	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-19 
Deposition Author(s): Yan, M., Zhang, H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-04-19
  Type: Initial release
  
• Version 1.1: 2023-08-30
  Changes: Data collection, Refinement description