8HQG | pdb_00008hqg

Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with inhibitor YH-53

• PDB DOI: https://doi.org/10.2210/pdb8HQG/pdb

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


• Deposited: 2022-12-13 Released: 2023-12-20 
• Deposition Author(s): Wang, J., Zhang, J., Li, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.264 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of main proteases of SARS-CoV-2 variants bound to a benzothiazole-based inhibitor.

Luo, J., Wang, W., Jiang, H., Li, W., Zeng, P., Wang, J., Zhou, X., Zou, X., Chen, S., Wang, Q., Zhang, J., Li, J.

(2023) Acta Biochim Biophys Sin (Shanghai) 55: 1257-1264

• PubMed: 37357528 
• DOI: https://doi.org/10.3724/abbs.2023053
• Primary Citation Related Structures: 
  8HQF, 8HQG, 8HQH, 8HQI, 8HQJ


• PubMed Abstract: 
  

  Main protease (M ^pro ) serves as an indispensable factor in the life cycle of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as well as its constantly emerging variants and is therefore considered an attractive target for antiviral drug development. Benzothiazole-based inhibitors targeting M ^pro have recently been investigated by several groups and proven to be promising leads for coronaviral drug development. In the present study, we determine the crystal structures of a benzothiazole-based inhibitor, YH-53, bound to M ^pro mutants from SARS-CoV-2 variants of concern (VOCs) or variants of interest (VOIs), including K90R (Beta, B.1.351), G15S (Lambda, C.37), Y54C (Delta, AY.4), M49I (Omicron, BA.5) and P132H (Omicron, B.1.1.529). The structures show that the benzothiazole group in YH-53 forms a C-S covalent bond with the sulfur atom of catalytic residue Cys145 in SARS-CoV-2 M ^pro mutants. Structural analysis reveals the key molecular determinants necessary for interaction and illustrates the binding mode of YH-53 to these mutant M ^pro s. In conclusion, structural insights from this study offer more information to develop benzothiazole-based drugs that are broader spectrum, more effective and safer.

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Organizational Affiliation: 
• College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China.
Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China.
School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China.
Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen 518118, China.
Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou 341000, China.
Nanchang Reproductive Hospital, Nanchang 330000, China.

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: 67.51 kDa 
• Atom Count: 4,622 
• Modeled Residue Count: 597 
• Deposited Residue Count: 598 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	299	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  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
HUR (Subject of Investigation/LOI)	C [auth A], D [auth B]	N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide C30 H33 N5 O5 S JBLLRCOZJMVOAE-HSQYWUDLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.264 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.127	α = 90
b = 99.033	β = 108.047
c = 59.32	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-20 
Deposition Author(s): Wang, J., Zhang, J., Li, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-12-20
  Type: Initial release
  
• Version 1.1: 2025-01-01
  Changes: Database references, Structure summary