8FY6 | pdb_00008fy6

SARS-CoV-2 main protease in complex with covalent inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8FY6/pdb

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


• Deposited: 2023-01-25 Released: 2023-08-30 
• Deposition Author(s): Fried, W., Chen, X.S.
• 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: 2.00 Å
• R-Value Free: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Alkyne as a Latent Warhead to Covalently Target SARS-CoV-2 Main Protease.

Ngo, C., Fried, W., Aliyari, S., Feng, J., Qin, C., Zhang, S., Yang, H., Shanaa, J., Feng, P., Cheng, G., Chen, X.S., Zhang, C.

(2023) J Med Chem 66: 12237-12248

• PubMed: 37595260 
• DOI: https://doi.org/10.1021/acs.jmedchem.3c00810
• Primary Citation Related Structures: 
  8FY6, 8FY7


• PubMed Abstract: 
  

  There is an urgent need for improved therapy to better control the ongoing COVID-19 pandemic. The main protease M ^pro plays a pivotal role in SARS-CoV-2 replications, thereby representing an attractive target for antiviral development. We seek to identify novel electrophilic warheads for efficient, covalent inhibition of M ^pro . By comparing the efficacy of a panel of warheads installed on a common scaffold against M ^pro , we discovered that the terminal alkyne could covalently modify M ^pro as a latent warhead. Our biochemical and X-ray structural analyses revealed the irreversible formation of the vinyl-sulfide linkage between the alkyne and the catalytic cysteine of M ^pro . Clickable probes based on the alkyne inhibitors were developed to measure target engagement, drug residence time, and off-target effects. The best alkyne-containing inhibitors potently inhibited SARS-CoV-2 infection in cell infection models. Our findings highlight great potentials of alkyne as a latent warhead to target cystine proteases in viruses and beyond.

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Organizational Affiliation: 
• Department of Chemistry and Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States.
Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States.
Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, United States.
Section of Infection and Immunity, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90089, United States.

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: 34.33 kDa 
• Atom Count: 2,543 
• Modeled Residue Count: 305 
• 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
YVZ (Subject of Investigation/LOI)	B [auth A]	(1R,2S,5S)-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-N-{(2R)-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-3-azabicyclo[3.1.0]hexane-2-carboxamide C24 H37 F3 N4 O4 QIKPVUMAJHNNAL-FHULIHMCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.455	α = 90
b = 63.276	β = 90
c = 103.843	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
Coot	model building
xia2	data scaling
xia2	data reduction
JBluIce-EPICS	data collection

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-30 
Deposition Author(s): Fried, W., Chen, X.S.

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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 AI150524

Revision History  

• Version 1.0: 2023-08-30
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Database references
• Version 2.0: 2024-07-24
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-10-23
  Changes: Structure summary