5ABJ

Structure of Coxsackievirus A16 in complex with GPP3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.305 
  • R-Value Observed: 0.305 

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This is version 1.1 of the entry. See complete history


Literature

Structure Elucidation of Coxsackievirus A16 in Complex with Gpp3 Informs a Systematic Review of Highly Potent Capsid Binders to Enteroviruses.

De Colibus, L.Wang, X.Tijsma, A.Neyts, J.Spyrou, J.A.B.Ren, J.Grimes, J.M.Puerstinger, G.Leyssen, P.Fry, E.E.Rao, Z.Stuart, D.I.

(2015) PLoS Pathog 11: 5165

  • DOI: https://doi.org/10.1371/journal.ppat.1005165
  • Primary Citation of Related Structures:  
    5ABJ

  • PubMed Abstract: 

    The replication of enterovirus 71 (EV71) and coxsackievirus A16 (CVA16), which are the major cause of hand, foot and mouth disease (HFMD) in children, can be inhibited by the capsid binder GPP3. Here, we present the crystal structure of CVA16 in complex with GPP3, which clarifies the role of the key residues involved in interactions with the inhibitor. Based on this model, in silico docking was performed to investigate the interactions with the two next-generation capsid binders NLD and ALD, which we show to be potent inhibitors of a panel of enteroviruses with potentially interesting pharmacological properties. A meta-analysis was performed using the available structural information to obtain a deeper insight into those structural features required for capsid binders to interact effectively and also those that confer broad-spectrum anti-enterovirus activity.


  • Organizational Affiliation

    Division of Structural Biology, University of Oxford, Oxford, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VP1297Coxsackievirus A16Mutation(s): 0 
UniProt
Find proteins for I3W9E1 (Coxsackievirus A16)
Explore I3W9E1 
Go to UniProtKB:  I3W9E1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3W9E1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VP2254Coxsackievirus A16Mutation(s): 0 
UniProt
Find proteins for I3W9E1 (Coxsackievirus A16)
Explore I3W9E1 
Go to UniProtKB:  I3W9E1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3W9E1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VP3242Coxsackievirus A16Mutation(s): 0 
UniProt
Find proteins for I3W9E1 (Coxsackievirus A16)
Explore I3W9E1 
Go to UniProtKB:  I3W9E1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3W9E1
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
VP469Coxsackievirus A16Mutation(s): 0 
UniProt
Find proteins for I3W9E1 (Coxsackievirus A16)
Explore I3W9E1 
Go to UniProtKB:  I3W9E1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3W9E1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YM2
Query on YM2

Download Ideal Coordinates CCD File 
F [auth A]1-[(3S)-5-[4-[(E)-ETHOXYIMINOMETHYL]PHENOXY]-3-METHYL-PENTYL]-3-PYRIDIN-4-YL-IMIDAZOLIDIN-2-ONE
C23 H30 N4 O3
IRYPPICIQPYQGY-YSRPOPIVSA-N
CL
Query on CL

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.305 
  • R-Value Observed: 0.305 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 491.6α = 90
b = 491.6β = 90
c = 709.56γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-11-04
    Changes: Database references