9CJQ | pdb_00009cjq

X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Ensitrelvir

• PDB DOI: https://doi.org/10.2210/pdb9CJQ/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-07-07 Released: 2025-07-09 
• Deposition Author(s): Esler, M.A., Shi, K., Harris, R.S., Aihara, H.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 
  0.258 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Ensitrelvir

Esler, M.A., Shi, K., Harris, R.S., Aihara, H.

To be published.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 137.9 kDa 
• Atom Count: 9,699 
• Modeled Residue Count: 1,208 
• Deposited Residue Count: 1,228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
main protease	A, B, C, D	307	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 4  Gene Names: rep, 1a-1b
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)	E [auth A], G [auth B], H [auth C], J [auth D]	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
EDO	F [auth A], I [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free:  0.258 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.022	α = 90
b = 106.994	β = 99.34
c = 116.522	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Esler, M.A., Shi, K., Harris, R.S., Aihara, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P01 CA214279
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R37 AI064064

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release