9PKR | pdb_00009pkr

SARS-CoV2 main protease bound to compound 26

• PDB DOI: https://doi.org/10.2210/pdb9PKR/pdb

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


• Deposited: 2025-07-14 Released: 2025-12-31 
• Deposition Author(s): Campbell, A.C., Krause, K.L., Opel-Reading, H.K.
• Funding Organization(s): Ministry of Business, Innovation and Employment (New Zealand)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.201 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Broad-Spectrum Peptidomimetic Inhibitors of Norovirus and Coronavirus 3C-like Proteases.

Brimble, M.A., Stubbing, L.A., Hermant, Y.O., Yang, S.H., Hubert, J.G., Pearl, E.S., McSweeney, A.M., Young, V.L., Campbell, A.C., Opel-Reading, H.K., McKenzie-Goldsmith, G.M., Putha, L., Mortuza, R., Wang, H., Hurst, B.L., Julander, J., Harris, L.D., Krause, K.L., Ward, V.K.

(2025) ACS Infect Dis 

• PubMed: 41412823 
• DOI: https://doi.org/10.1021/acsinfecdis.5c00680
• Primary Citation of Related Structures:  
  9PJF, 9PJG, 9PKR


• PubMed Abstract: 
  

  The cysteine 3C-like proteases (3CL ^pro ) of caliciviruses, coronaviruses, and picornaviruses are essential for viral replication. In this study, we report the development of potent broad-spectrum peptidomimetic antiviral agents that target the 3CL ^pro of caliciviruses (NS6), coronaviruses (M ^pro ), and a picornavirus (3C). Based upon previously reported inhibitors, a small library of compounds was designed, synthesized and tested to identify a core structure, which was then derivatized with a focus upon P3 and P4 positions to afford new inhibitors with improved potency against the respective viral enzymes and enhanced binding as determined by X-ray crystallography. These compounds were tested against a range of viruses in culture, revealing minimal toxicity while exhibiting broad-spectrum potent nanomolar activities against noroviruses and several coronavirus species, including alpha and omicron variants of SARS-CoV-2 and Middle East Respiratory Syndrome virus (MERS).

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Organizational Affiliation: 
• School of Chemical Sciences, School of Biological Sciences, The University of Auckland, 23 Symonds Street, 3b Symonds Street, Auckland 1142, New Zealand.
Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3b Symonds Street, Auckland 1142, New Zealand.
Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, P.O. Box 56, 720 Cumberland Street, Dunedin 9054, New Zealand.
Department of Biochemistry, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin 9054, New Zealand.
Institute for Antiviral Research, Utah State University, 5600 Old Main Hill, Logan, Utah. 84322-5600, United States.
Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Road, Lower Hutt 5010, New Zealand.

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: 68.92 kDa 
• Atom Count: 5,386 
• Modeled Residue Count: 616 
• Deposited Residue Count: 616 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	305	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
(BOC)F(ALC)(ELL) peptide	C [auth E], D [auth F]	3	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], G [auth B], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1C3V	C [auth E], D [auth F]	L-PEPTIDE LINKING	C14 H19 N O4		PHE
ALC	C [auth E], D [auth F]	L-PEPTIDE LINKING	C9 H17 N O2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.201 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.67	α = 90
b = 106.298	β = 103.647
c = 54.47	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Campbell, A.C., Krause, K.L., Opel-Reading, H.K.

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Funding Organization	Location	Grant Number
Ministry of Business, Innovation and Employment (New Zealand)	New Zealand	UOOX1904

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release