8U40 | pdb_00008u40

Crystal structure of main protease of SARS-CoV-2 complexed with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8U40/pdb

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


• Deposited: 2023-09-08 Released: 2025-03-12 
• Deposition Author(s): Chen, P., Arutyunova, E., Lu, J., Young, H.S., Lemieux, M.J.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.274 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Literature

Crystal structure of main protease of SARS-CoV-2 complexed with inhibitor

Chen, P., Arutyunova, E., Lu, J., Young, H.S., Lemieux, M.J.

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)

Macromolecule Content 

• Total Structure Weight: 68.56 kDa 
• Atom Count: 4,887 
• Modeled Residue Count: 611 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V8X (Subject of Investigation/LOI)	C [auth A], D [auth B]	N-[(2S)-3-cyclopropyl-1-({(1E,2R)-1-imino-3-[(3R)-2-oxo-2,3-dihydropyridin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]-5,7-difluoro-1H-indole-2-carboxamide C23 H23 F2 N5 O3 BPEXUOKHFCNFEQ-JVXBGGSJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.274 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.11	α = 90
b = 54.093	β = 101.64
c = 113.458	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Chen, P., Arutyunova, E., Lu, J., Young, H.S., Lemieux, M.J.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release