8J34 | pdb_00008j34

Crystal structure of MERS main protease in complex with PF00835231

• PDB DOI: https://doi.org/10.2210/pdb8J34/pdb

• Classification: VIRAL PROTEIN/INHIBITOR
• Organism(s): Middle East respiratory syndrome-related coronavirus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2023-04-16 Released: 2024-04-17 
• Deposition Author(s): Zhou, X.L., Lin, C., Zou, X.F., Zhang, J., Li, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.255 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Structural basis for the inhibition of coronaviral main proteases by PF-00835231.

Zhou, X., Lu, X., Lin, C., Zou, X., Li, W., Zeng, X., Wang, J., Zeng, P., Wang, W., Zhang, J., Jiang, H., Li, J.

(2024) Acta Biochim Biophys Sin (Shanghai) 56: 1813-1822

• PubMed: 39076076 
• DOI: https://doi.org/10.3724/abbs.2024122
• Primary Citation Related Structures: 
  8J32, 8J34, 8J35, 8J36, 8J37, 8J38, 8J39, 8J3A, 8J3B


• PubMed Abstract: 
  

  The main protease (M ^pro ) of coronaviruses plays a key role in viral replication, thus serving as a hot target for drug design. PF-00835231 is a promising inhibitor of SARS-CoV-2 M ^pro . Here, we report the inhibitory potency of PF-00835231 against SARS-CoV-2 M ^pro and seven M ^pro mutants (G15S, M49I, Y54C, K90R, P132H, S46F, and V186F) from SARS-CoV-2 variants. The results confirm that PF-00835231 has broad-spectrum inhibition against various coronaviral M ^pro s. In addition, the crystal structures of SARS-CoV-2 M ^pro , SARS-CoV M ^pro , MERS-CoV M ^pro , and seven SARS-CoV-2 M ^pro mutants (G15S, M49I, Y54C, K90R, P132H, S46F, and V186F) in complex with PF-00835231 are solved. A detailed analysis of these structures reveals key determinants essential for inhibition and elucidates the binding modes of different coronaviral M ^pro s. Given the importance of the main protease for the treatment of coronaviral infection, structural insights into M ^pro inhibition by PF-00835231 can accelerate the design of novel antivirals with broad-spectrum efficacy against different human coronaviruses.

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Organizational Affiliation: 
• College of Pharmacy, Gannan Medical University, Ganzhou 341000, China.
Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen 518118, China.
Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou 341000, China.
Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China.
School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, 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: 66.34 kDa 
• Atom Count: 4,675 
• Modeled Residue Count: 597 
• Deposited Residue Count: 598 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF1a	A, B	299	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0  Gene Names: orf1a
UniProt
Find proteins for K9N7C7 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)) Explore K9N7C7  Go to UniProtKB:  K9N7C7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V2M (Subject of Investigation/LOI)	C [auth A], D [auth B]	N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide C24 H34 N4 O6 FDQSUXUTXIGUIA-PRIDNEQBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.255 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.902	α = 90
b = 91.33	β = 90
c = 118.135	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: 2024-04-17 
Deposition Author(s): Zhou, X.L., Lin, C., Zou, X.F., Zhang, J., Li, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary
• Version 1.2: 2025-05-07
  Changes: Database references