9IPP | pdb_00009ipp

Crystal structure of MERS main protease in complex with carmofur

• PDB DOI: https://doi.org/10.2210/pdb9IPP/pdb

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


• Deposited: 2024-07-11 Released: 2025-07-16 
• Deposition Author(s): Guo, L., Zhou, X.L., Zeng, P., Li, W.W., Zhang, J., Li, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.227 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Structural basis of main proteases of MERS-CoV bound to antineoplastic drug carmofur.

Guo, L., Zeng, P., Zhou, X., Li, W., Zhang, J., Li, J.

(2024) Biochem Biophys Res Commun 735: 150469-150469

• PubMed: 39106601 
• DOI: https://doi.org/10.1016/j.bbrc.2024.150469
• Primary Citation of Related Structures:  
  9IPP


• PubMed Abstract: 
  

  Recurrent epidemics of coronaviruses have posed significant threats to human life and health. The mortality rate of patients infected with the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is 35 %. The main protease (M ^pro ) plays a crucial role in the MERS-CoV life cycle, and M ^pro exhibited a high degree of conservation among different coronaviruses. Therefore inhibition of M ^pro has become an effective strategy for the development of broad-spectrum anti-coronaviral drugs. The inhibition of SARS-CoV-2 M ^pro by the anti-tumor drug carmofur has been revealed, but structural studies of carmofur in complex with M ^pro from other types of coronavirus have not been reported. Hence, we revealed the structure of the MERS-CoV M ^pro -carmofur complex, analysed the structural basis for the binding of carmofur to MERS-CoV M ^pro in detail, and compared the binding patterns of carmofur to M ^pro s of two different coronaviruses, MERS-CoV and SARS-CoV-2. Considering the importance of M ^pro s for coronavirus therapy, structural understanding of M ^pro inhibition by carmofur could contribute to the design and development of novel antiviral drugs with safe and broad-spectrum efficacy.

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Organizational Affiliation: 
• Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen, China.
Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou, China.
Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen, China; Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou, China. Electronic address: [e-mail].
Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen, China; Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou, China. Electronic address: [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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 65.8 kDa 
• Atom Count: 4,777 
• Modeled Residue Count: 600 
• Deposited Residue Count: 600 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	300	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0  EC: 3.4.19.12 (PDB Primary Data), 3.4.22.69 (PDB Primary Data)
UniProt
Find proteins for T2BB45 (Middle East respiratory syndrome-related coronavirus) Explore T2BB45  Go to UniProtKB:  T2BB45

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JRY (Subject of Investigation/LOI)	C [auth A], D [auth B]	hexylcarbamic acid C7 H15 N O2 YAQPZDICKJDHTR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.227 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.811	α = 90
b = 95.066	β = 90
c = 97.441	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: 2025-07-16 
Deposition Author(s): Guo, L., Zhou, X.L., Zeng, P., Li, W.W., Zhang, J., Li, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release
  
• Version 1.1: 2026-01-28
  Changes: Database references