9P6F | pdb_00009p6f

Structure of the SARS-CoV-2 main protease in complex with inhibitor SR-B-78

• PDB DOI: https://doi.org/10.2210/pdb9P6F/pdb

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


• Deposited: 2025-06-18 Released: 2026-03-04 
• Deposition Author(s): Blankenship, L.R., Liu, W.R.
• Funding Organization(s): Welch Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.303 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.268 (Depositor), 0.268 (DCC) 
• R-Value Observed: 
  0.269 (Depositor) 

Starting Model: experimental

Literature

From nicotine to SARS-CoV-2 antivirals with potent in vivo efficacy and a broad anti-coronavirus spectrum.

Khatua, K., Atla, S., Coleman, D., Blankenship, L.R., Alugubelli, Y.R., Vulupala, V., Guo, X.S., Xia, H., Kalveram, B.K., Walker, D.H., Hurst, B.L., Kumar, S., Cho, C.D., Sharma, S., Yang, K., Rabie, D., Nyalata, S., Neuman, B.W., Xie, X., Xu, S., Liu, W.R.

(2026) Nat Commun 17

• PubMed: 41690944 
• DOI: https://doi.org/10.1038/s41467-026-69527-5
• Primary Citation Related Structures: 
  9P6F


• PubMed Abstract: 
  

  Anecdotal reports about smoking that might prevent SARS-CoV-2 infection inspire the search for nicotine and its pyrolysis products as inhibitors of the SARS-CoV-2 main protease (M ^Pro ). This effort leads to the discovery of 3-vinylpyridine as an M ^Pro inhibitor. 3-Vinylpyridine resembles part of nirmatrelvir in binding to M ^Pro but does not involve a critical interaction with residue E166, whose mutation has led to resistance to nirmatrelvir. Integration of the two molecules, followed by a medicinal chemistry campaign, produces several molecules with better in vitro potency than nirmatrelvir. Two lead molecules, YR-C-136 and SR-B-103, display better pharmacokinetic characteristics than nirmatrelvir in virus-challenged male mice and much better antiviral efficacy in virus-challenged female mice. Both molecules maintain high potency in inhibiting the nirmatrelvir-resistant M ^Pro (E166V/L50F) variant. They also exhibit a broad and highly potent antiviral spectrum against most pathogenic coronaviruses. With high in vivo potency, both molecules are potentially standalone pan-antivirals for coronaviruses and may serve as countermeasures for future coronavirus outbreaks.

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Organizational Affiliation: 
• Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX, USA.
Department of Microbiology and Immunology, the University of Texas Medical Branch, Galveston, TX, USA.
Department of Pathology, the University of Texas Medical Branch, Galveston, TX, USA.
Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA.
Texas A&M Global Health Research Complex of Biology and Department of Biology, College of Arts and Sciences, Texas A&M University, College Station, TX, USA.
Texas A&M Global Health Research Complex of Biology and Department of Biology, College of Arts and Sciences, Texas A&M University, College Station, TX, USA. [e-mail].
Department of Microbiology and Immunology, the University of Texas Medical Branch, Galveston, TX, USA. [e-mail].
Sealy Institute for Drug Discovery, the University of Texas Medical Branch, Galveston, TX, USA. [e-mail].
Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX, USA. [e-mail].
Department of Pharmaceutical Sciences, Irma Lerma College of Pharmacy, Texas A&M University, College Station, TX, USA. [e-mail].
Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX, USA. [e-mail].
Department of Pharmaceutical Sciences, Irma Lerma College of Pharmacy, Texas A&M University, College Station, TX, USA. [e-mail].
Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, USA. [e-mail].
Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, TX, USA. [e-mail].
Department of Cell Biology and Genetics, College of Medicine, Texas A&M University, College Station, TX, USA. [e-mail].

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: 34.34 kDa 
• Atom Count: 2,403 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CG8 (Subject of Investigation/LOI)	B [auth A]	(1R,2S,5S)-N-[(1S,2Z)-2-imino-1-(5-methoxypyridin-3-yl)ethyl]-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide C24 H32 F3 N5 O4 ATTSVIKVVHABCD-VCLVVCANSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.303 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.268 (Depositor), 0.268 (DCC) 
• R-Value Observed: 0.269 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.65	α = 90
b = 81.281	β = 97.392
c = 90.448	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PROTEUM PLUS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-03-04 
Deposition Author(s): Blankenship, L.R., Liu, W.R.

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Funding Organization	Location	Grant Number
Welch Foundation	United States	--

Revision History  

• Version 1.0: 2026-03-04
  Type: Initial release
  
• Version 1.1: 2026-04-08
  Changes: Database references