9KQV | pdb_00009kqv

Cryo-EM structure of MPXV core protease in complex with aloxistatin(E64d)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Resolution: 2.93 Å
  • Resolution: 2.93 Å
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Substrate recognition and cleavage mechanism of the monkeypox virus core protease.

Gao, Y.Xie, X.Zhang, X.Cao, J.Lan, W.You, T.Li, D.Dong, X.Dai, W.Xiang, Y.Hu, S.Shang, W.Wu, B.Zhang, Y.Xu, J.Liu, X.Wang, H.Hu, W.Zhang, M.Duan, Y.Cui, W.Zhou, H.Mao, S.Jia, H.Sun, Z.Jia, M.Yin, Y.Nguyen, H.C.Yang, K.Yang, B.Yang, X.Ji, X.Xiao, G.Wang, W.Zhang, L.Rao, Z.Liu, H.Yang, H.

(2025) Nature 

  • DOI: https://doi.org/10.1038/s41586-025-09014-x
  • Primary Citation of Related Structures:  
    9JAL, 9JAM, 9JAN, 9JAQ, 9KQV, 9KR6

  • PubMed Abstract: 

    Poxviruses cause severe diseases, including smallpox and mpox, that pose major threats to human health. The poxvirus core protease (Core Pro ) is essential for viral maturation and is highly conserved in poxviruses, making it an attractive antiviral target 1 . However, the structure of Core Pro remains unknown, hampering antiviral development. Here we determined the apo structure of monkeypox virus (MPXV) Core Pro and the structure of Core Pro in a complex with the inhibitor aloxistatin, a drug candidate for muscular dystrophy 2 . These structures show that Core Pro forms a homodimer that features a unique 'dancing couple' fold. The catalytic intermediate state of Core Pro was characterized by an aldehyde derivative from a natural substrate (I-G18). This derivative binds covalently to the catalytic Cys328, shifting the active site of the viral protease from a closed conformation in the apo form to a favourable open conformation upon substrate binding. On the basis of the Core Pro -I-G18 complex, we designed a series of peptidomimetic inhibitors with a nitrile warhead, which could covalently anchor with the catalytic Cys328. These compounds inhibit Core Pro with half-maximal inhibitory concentrations of 44.9-100.3 nM, and exhibit potent and broad anti-poxvirus activity. Our studies provide a basis for designing wide-spectrum inhibitors against poxvirus infections.


  • Organizational Affiliation

    Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Core protease I7
A, B
423Monkeypox virusMutation(s): 0 
Gene Names: 
EC: 3.4.22
UniProt
Find proteins for Q5IXV7 (Monkeypox virus)
Explore Q5IXV7 
Go to UniProtKB:  Q5IXV7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5IXV7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E6D (Subject of Investigation/LOI)
Query on E6D

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate
C17 H32 N2 O5
FGRTVYZNNRCSAS-KBPBESRZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Resolution: 2.93 Å
  • Resolution: 2.93 Å
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81902063

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-06-25
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-02
    Changes: Data collection, Database references