9ZO3 | pdb_00009zo3

X-ray structure of SARS-CoV-2 main protease covalently bound to inhibitor GRL-062-22 at 1.65 A

• PDB DOI: https://doi.org/10.2210/pdb9ZO3/pdb

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


• Deposited: 2025-12-15 Released: 2025-12-24 
• Deposition Author(s): Mesecar, A.D., Lendy, E.K., Jayashankar, U., Bogan, S.N., Center for Structural Biology of Infectious Diseases (CSBID), Ghosh, A.K.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.196 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of SARS-CoV-2 main protease covalently bound to inhibitor GRL-062-22 at 1.65 A

Mesecar, A.D., Lendy, E.K., Jayashankar, U., Bogan, S.N., Center for Structural Biology of Infectious Diseases (CSBID), Ghosh, A.K.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.52 kDa 
• Atom Count: 2,887 
• Modeled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	306	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
A1C3M	B [auth A]	(3S)-N-{(1S,2S)-1-(1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopiperidin-3-yl]propan-2-yl}-2-[3-methyl-N-(trifluoroacetyl)-L-valyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxamide C33 H38 F3 N5 O5 S DBFUHXJHDXLDQC-IXCSSYKCSA-N
NA (Subject of Investigation/LOI)	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.196 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.958	α = 90
b = 63.229	β = 90
c = 105.517	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Mesecar, A.D., Lendy, E.K., Jayashankar, U., Bogan, S.N., Center for Structural Biology of Infectious Diseases (CSBID), Ghosh, A.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1RO1 AI158649
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM132024

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release
  
• Version 1.1: 2026-01-14
  Changes: Database references, Structure summary
• Version 1.2: 2026-03-25
  Changes: Database references, Other, Structure summary