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)

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)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Identification of a Potent Pan-Coronaviral Main Protease Inhibitor

Chen, P., Strunk, U., Arutyunova, E., Lu, J., Chen, S.A., Demmon, S., Maplethorpe, C., Kandadai, A.S., Shields, J., Saffran, H.A., Lamer, T., Fischer, C., Van Oers, T.J., Turner, Z., Leong, P., Iyyathurai, J., Young, H.S., Bai, B., Vederas, J.C., Nieman, J.A., Joyce, M.A., Tyrrell, D.L., Lemieux, M.J.

(2026) J Med Chem

DOI: https://doi.org/10.1021/acs.jmedchem.6c00645

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
V8X (Subject of Investigation/LOI) Query on V8X Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	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		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-12

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-03-12
Type: Initial release
Version 1.1: 2026-07-22
Changes: Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.