5DP4

Crystal Structure of EV71 3C Proteinase in complex with compound 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Fragment-wise design of inhibitors to 3C proteinase from enterovirus 71

Wu, C.Zhang, L.Li, P.Cai, Q.Peng, X.Yin, K.Chen, X.Ren, H.Zhong, S.Weng, Y.Guan, Y.Chen, S.Wu, J.Li, J.Lin, T.

(2016) Biochim Biophys Acta 1860: 1299-1307

  • DOI: https://doi.org/10.1016/j.bbagen.2016.03.017
  • Primary Citation of Related Structures:  
    5DP3, 5DP4, 5DP5, 5DP6, 5DP7, 5DP8, 5DP9, 5DPA

  • PubMed Abstract: 

    Enterovirus 71 (EV71) is a causative agent of hand, foot and mouth disease (HFMD), which can spread its infection to central nervous and other systems with severe consequence. A key factor in the replication of EV71 is its 3C proteinase (3C(pro)), a significant drug target. Peptidomimetics were employed as inhibitors of this enzyme for developing antivirals. However, the peptide bonds in these peptidomimetics are a source of low bioavailability due to their susceptibility to protease digestion. To produce non-peptidomimetic inhibitors by replacing these peptide bonds, it would be important to gain better understanding on the contribution of each component to the interaction and potency. A series of compounds of different lengths targeting 3C(pro) and having an α,β-unsaturated ester as the warhead were synthesized and their interactions with the enzyme were evaluated by complex structure analyses and potency assays for a better understanding on the relationship between potency and evolution of interaction. The P2 moiety of the compound would need to be oriented to interact in the S2 site in the substrate binding cleft and the P3-P4 moieties were required to generate sufficient potency. A hydrophobic terminal group will benefit the cellular uptake and improve the activity in vivo. The data presented here provide a basis for designing a new generation of non-peptidomimetics to target EV71 3C(pro).


  • Organizational Affiliation

    The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China; State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State-Province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life Sciences, Xiamen University, Xiamen, Fujian, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C proteinase
A, B, C, D
192Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for A9XG43 (Human enterovirus 71)
Explore A9XG43 
Go to UniProtKB:  A9XG43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9XG43
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.894α = 90
b = 75.456β = 90
c = 128.885γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2016-04-06
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description