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 

wwPDB Validation 3D Report Full Report


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: 10.1371/journal.ppat.1005165

  • 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 comp ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VP1
A
297Coxsackievirus A16Mutation(s): 0 
Find proteins for I3W9E1 (Coxsackievirus A16)
Go to UniProtKB:  I3W9E1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VP2
B
254Coxsackievirus A16Mutation(s): 0 
Find proteins for I3W9E1 (Coxsackievirus A16)
Go to UniProtKB:  I3W9E1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VP3
C
242Coxsackievirus A16Mutation(s): 0 
Find proteins for I3W9E1 (Coxsackievirus A16)
Go to UniProtKB:  I3W9E1
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
VP4
D
69Coxsackievirus A16Mutation(s): 0 
Find proteins for I3W9E1 (Coxsackievirus A16)
Go to UniProtKB:  I3W9E1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YM2
Query on YM2

Download SDF File 
Download CCD File 
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
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.305 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 491.600α = 90.00
b = 491.600β = 90.00
c = 709.560γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSphasing
HKL-2000data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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