9EET | pdb_00009eet

Crystal structure of the SARS-CoV-2 nsp5 main protease (Mpro) E166V mutant in complex with inhibitor GC376

• PDB DOI: https://doi.org/10.2210/pdb9EET/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-11-19 Released: 2025-06-18 
• Deposition Author(s): Neilsen, G., Kirby, K.A., Sarafianos, S.G.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.229 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Strategy to overcome a nirmatrelvir resistance mechanism in the SARS-CoV-2 nsp5 protease.

Neilsen, G., Lan, S., Slack, R.L., Lorson, Z.C., Emanuelli Castaner, A., Lee, R., Edwards, K.G., Zhang, H., Lee, J., Cantara, W.A., Cilento, M.E., Zhang, H., De, R., Amblard, F., Tedbury, P.R., Kirby, K.A., Schinazi, R.F., Sarafianos, S.G.

(2025) Sci Adv 11: eadv8875-eadv8875

• PubMed: 40479048 
• DOI: https://doi.org/10.1126/sciadv.adv8875
• Primary Citation Related Structures: 
  9EEI, 9EET, 9EEV


• PubMed Abstract: 
  

  E166V in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nsp5 protease confers strong resistance to the antiviral component of Paxlovid, nirmatrelvir (NIR), in passaging and clinical samples. In SARS-CoV-2 replicons, E166V drastically decreased Washington (WA1) but not Omicron (BA.1) fitness (20- versus 2-fold), suggesting a lower barrier to resistance in the BA.1 strain and consistent with observed differences in respective nsp5 dimerization affinities. Crystal structures reveal a steric clash between the rigid, bulky NIR tert -butyl group and the β-branched Val ¹⁶⁶ , disrupting the covalent binding of NIR to the catalytic Cys ¹⁴⁵ and leading to high resistance in BA.1 and WA1 replicons. NIR-resistant replicons remained susceptible to GC376, which can still covalently bind Cys ¹⁴⁵ by avoiding a steric clash with Val ¹⁶⁶ through "wiggling and jiggling." Hence, strategic flexibility is a strategy that will help design second-generation antivirals against NIR-resistant viruses.

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Organizational Affiliation: 
• Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.
Children's Healthcare of Atlanta, Atlanta, GA 30322, USA.

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: light scattering

Macromolecule Content 

• Total Structure Weight: 34.2 kDa 
• Atom Count: 2,503 
• 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): 1  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
UED (Subject of Investigation/LOI)	B [auth A]	N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide C21 H31 N3 O5 JUCVXDDMQHPCKT-BZSNNMDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.229 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.097	α = 90
b = 53.533	β = 100.84
c = 113.68	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Neilsen, G., Kirby, K.A., Sarafianos, S.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI167356

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release