7TUU | pdb_00007tuu

Structure of the SARS-CoV-2 main protease in complex with halicin

• PDB DOI: https://doi.org/10.2210/pdb7TUU/pdb

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


• Deposited: 2022-02-03 Released: 2022-08-03 
• Deposition Author(s): Yang, K.S., Liu, W.R.
• Funding Organization(s): Welch Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.272 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Starting Model: experimental

Literature

Repurposing Halicin as a potent covalent inhibitor for the SARS-CoV-2 main protease.

Yang, K.S., Alex Kuo, S.T., Blankenship, L.R., Geng, Z.Z., Li, S.G., Russell, D.H., Yan, X., Xu, S., Liu, W.R.

(2022) Curr Res Chem Biol 2: 100025-100025

• PubMed: 35815070 
• DOI: https://doi.org/10.1016/j.crchbi.2022.100025
• Primary Citation Related Structures: 
  7TUU


• PubMed Abstract: 
  

  The rapid spread of COVID-19 has caused a worldwide public health crisis. For prompt and effective development of antivirals for SARS-CoV-2, the pathogen of COVID-19, drug repurposing has been broadly conducted by targeting the main protease (M ^Pro ), a key enzyme responsible for the replication of virus inside the host. In this study, we evaluate the inhibition potency of a nitrothiazole-containing drug, halicin, and reveal its reaction and interaction mechanism with M ^Pro . The in vitro potency test shows that halicin inhibits the activity of M ^Pro an IC ₅₀ of 181.7 ​nM. Native mass spectrometry and X-ray crystallography studies clearly indicate that the nitrothiazole fragment of halicin covalently binds to the catalytic cysteine C145 of M ^Pro . Interaction and conformational changes inside the active site of M ^Pro suggest a favorable nucleophilic aromatic substitution reaction mechanism between M ^Pro C145 and halicin, explaining the high inhibition potency of halicin towards M ^Pro .

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Organizational Affiliation: 
• Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.
Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, 77030, USA.
Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX, 77843, 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: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.22 kDa 
• Atom Count: 2,580 
• 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  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
U88 (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A]	5-nitro-1,3-thiazole C3 H2 N2 O2 S VVVCJCRUFSIVHI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.272 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.213	α = 90
b = 84.362	β = 95.608
c = 90.093	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: 2022-08-03 
Deposition Author(s): Yang, K.S., Liu, W.R.

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Funding Organization	Location	Grant Number
Welch Foundation	United States	--

Revision History  

• Version 1.0: 2022-08-03
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary