3ZFE

Human enterovirus 71 in complex with capsid binding inhibitor WIN51711


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 

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


Literature

Structure of Human Enterovirus 71 in Complex with a Capsid-Binding Inhibitor.

Plevka, P.Perera, R.Yap, M.L.Cardosa, J.Kuhn, R.J.Rossmann, M.G.

(2013) Proc Natl Acad Sci U S A 110: 5463

  • DOI: https://doi.org/10.1073/pnas.1222379110
  • Primary Citation of Related Structures:  
    3ZFE, 3ZFF, 3ZFG

  • PubMed Abstract: 

    Human enterovirus 71 is a picornavirus causing hand, foot, and mouth disease that may progress to fatal encephalitis in infants and small children. As of now, no cure is available for enterovirus 71 infections. Small molecule inhibitors binding into a hydrophobic pocket within capsid viral protein 1 were previously shown to effectively limit infectivity of many picornaviruses. Here we report a 3.2-Å-resolution X-ray structure of the enterovirus 71 virion complexed with the capsid-binding inhibitor WIN 51711. The inhibitor replaced the natural pocket factor within the viral protein 1 pocket without inducing any detectable rearrangements in the structure of the capsid. Furthermore, we show that the compound stabilizes enterovirus 71 virions and limits its infectivity, probably through restricting dynamics of the capsid necessary for genome release. Thus, our results provide a structural basis for development of antienterovirus 71 capsid-binding drugs.


  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-2032, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VP1298Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for A9X4C2 (Human enterovirus 71)
Explore A9X4C2 
Go to UniProtKB:  A9X4C2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9X4C2
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 A9X4C2 (Human enterovirus 71)
Explore A9X4C2 
Go to UniProtKB:  A9X4C2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9X4C2
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 A9X4C2 (Human enterovirus 71)
Explore A9X4C2 
Go to UniProtKB:  A9X4C2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9X4C2
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPH
Query on SPH

Download Ideal Coordinates CCD File 
E [auth A]SPHINGOSINE
C18 H37 N O2
WWUZIQQURGPMPG-MSOLQXFVSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

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F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth B],
K [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 594.5α = 90
b = 594.5β = 90
c = 594.5γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
GLRFphasing
PHASERphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-04-10
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description