5C1X

Crystal structure of EV71 3C Proteinase in complex with Compound VIII


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Optimize the interactions at S4 with efficient inhibitors targeting 3C proteinase from enterovirus 71

Zhang, L.Huang, G.Cai, Q.Zhao, C.Tang, L.Ren, H.Li, P.Li, N.Huang, J.Chen, X.Guan, Y.You, H.Chen, S.Li, J.Lin, T.

(2016) J Mol Recognit 29: 520-527

  • DOI: https://doi.org/10.1002/jmr.2551
  • Primary Citation of Related Structures:  
    5C1U, 5C1X, 5C1Y, 5C20

  • PubMed Abstract: 

    Enterovirus 71 (EV71) is the causative agent of hand, foot and mouth disease and can spread its infections to the central nervous and other systems with severe consequences. The replication of EV71 depends on its 3C proteinase (3C pro ), a significant drug target. By X-ray crystallography and functional assays, the interactions between inhibitors and EV71 3C pro were evaluated. It was shown that improved interactions at S4 for the substrate binding could significantly enhance the potency. A new series of potent inhibitors with high ligand efficiency was generated for developing antivirals to treat and control the EV71-associated diseases. Copyright © 2016 John Wiley & Sons, Ltd.


  • Organizational Affiliation

    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
192Enterovirus A71Mutation(s): 0 
EC: 3.4.22.28
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GHX
Query on GHX

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(phenylmethyl) N-[(2S)-1-oxidanylidene-1-[[(2S)-1-oxidanyl-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-3-phenyl-propan-2-yl]carbamate
C24 H29 N3 O5
SDSQZWABGUFEMG-ACRUOGEOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.948α = 90
b = 64.084β = 91.11
c = 76.489γ = 90
Software Package:
Software NamePurpose
AUTOMARdata reduction
AUTOMARdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-10-26
    Changes: Database references
  • Version 2.0: 2020-09-02
    Changes: Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description