4CDQ

Crystal structure of human Enterovirus 71 in complex with the uncoating inhibitor GPP2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

More-Powerful Virus Inhibitors from Structure-Based Analysis of Hev71 Capsid-Binding Molecules

De Colibus, L.Wang, X.Spyrou, J.A.B.Kelly, J.Ren, J.Grimes, J.Puerstinger, G.Stonehouse, N.Walter, T.S.Hu, Z.Wang, J.Li, X.Peng, W.Rowlands, D.J.Fry, E.E.Rao, Z.Stuart, D.I.

(2014) Nat Struct Mol Biol 21: 282

  • DOI: https://doi.org/10.1038/nsmb.2769
  • Primary Citation of Related Structures:  
    4CDQ, 4CDU, 4CDW, 4CDX, 4CEW, 4CEY

  • PubMed Abstract: 

    Enterovirus 71 (HEV71) epidemics in children and infants result mainly in mild symptoms; however, especially in the Asia-Pacific region, infection can be fatal. At present, no therapies are available. We have used structural analysis of the complete virus to guide the design of HEV71 inhibitors. Analysis of complexes with four 3-(4-pyridyl)-2-imidazolidinone derivatives with varying anti-HEV71 activities pinpointed key structure-activity correlates. We then identified additional potentially beneficial substitutions, developed methods to reliably triage compounds by quantum mechanics-enhanced ligand docking and synthesized two candidates. Structural analysis and in vitro assays confirmed the predicted binding modes and their ability to block viral infection. One ligand (with IC50 of 25 pM) is an order of magnitude more potent than the best previously reported inhibitor and is also more soluble. Our approach may be useful in the design of effective drugs for enterovirus infections.


  • Organizational Affiliation

    Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VP1297Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for B2ZUN0 (Human enterovirus 71)
Explore B2ZUN0 
Go to UniProtKB:  B2ZUN0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2ZUN0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VP2254Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for B2ZUN0 (Human enterovirus 71)
Explore B2ZUN0 
Go to UniProtKB:  B2ZUN0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2ZUN0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VP3242Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for B2ZUN0 (Human enterovirus 71)
Explore B2ZUN0 
Go to UniProtKB:  B2ZUN0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2ZUN0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
VP469Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for B2ZUN0 (Human enterovirus 71)
Explore B2ZUN0 
Go to UniProtKB:  B2ZUN0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2ZUN0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7VR
Query on 7VR

Download Ideal Coordinates CCD File 
E [auth A]4-((5-(2-oxo-3-(pyridin-4-yl)imidazolidin-1-yl)pentyl)oxy)benzaldehyde O-ethyl oxime
C22 H28 N4 O3
TVKWRLSBRIRPDH-HKOYGPOVSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 599.769α = 90
b = 599.769β = 90
c = 599.769γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-02-19
    Changes: Database references
  • Version 1.2: 2014-03-19
    Changes: Database references
  • Version 1.3: 2015-08-19
    Changes: Other
  • Version 1.4: 2019-01-30
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2019-02-06
    Changes: Data collection, Experimental preparation