9CJR | pdb_00009cjr

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

PDB DOI: https://doi.org/10.2210/pdb9CJR/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.215 (Depositor), 0.215 (DCC)
R-Value Work:
0.174 (Depositor), 0.174 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 68.29 kDa
Atom Count: 5,058
Modeled Residue Count: 601
Deposited Residue Count: 608
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	304	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 2 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7YY (Subject of Investigation/LOI) Query on 7YY Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [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		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.215 (Depositor), 0.215 (DCC)
R-Value Work: 0.174 (Depositor), 0.174 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.437	α = 90
b = 99.397	β = 105.76
c = 57.077	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-09

Deposition Author(s):

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