6TSD

Crystal structure of human coxsackievirus A24v in complex with pentavalent inhibitor ME0752

  • Classification: VIRUS
  • Organism(s): Coxsackievirus A24
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2019-12-20 Released: 2021-07-07 
  • Deposition Author(s): Zocher, G., Stehle, T.
  • Funding Organization(s): German Research Foundation (DFG), German Federal Ministry for Education and Research, Knut and Alice Wallenberg Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Work: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Pentavalent Sialic Acid Conjugates Block Coxsackievirus A24 Variant and Human Adenovirus Type 37-Viruses That Cause Highly Contagious Eye Infections.

Johansson, E.Caraballo, R.Mistry, N.Zocher, G.Qian, W.Andersson, C.D.Hurdiss, D.L.Chandra, N.Thompson, R.Frangsmyr, L.Stehle, T.Arnberg, N.Elofsson, M.

(2020) ACS Chem Biol 15: 2683-2691

  • DOI: https://doi.org/10.1021/acschembio.0c00446
  • Primary Citation of Related Structures:  
    6TSD

  • PubMed Abstract: 

    Coxsackievirus A24 variant (CVA24v) and human adenovirus 37 (HAdV-37) are leading causative agents of the severe and highly contagious ocular infections acute hemorrhagic conjunctivitis and epidemic keratoconjunctivitis, respectively. Currently, neither vaccines nor antiviral agents are available for treating these diseases, which affect millions of individuals worldwide. CVA24v and HAdV-37 utilize sialic acid as attachment receptors facilitating entry into host cells. Previously, we and others have shown that derivatives based on sialic acid are effective in preventing HAdV-37 binding and infection of cells. Here, we designed and synthesized novel pentavalent sialic acid conjugates and studied their inhibitory effect against CVA24v and HAdV-37 binding and infection of human corneal epithelial cells. The pentavalent conjugates are the first reported inhibitors of CVA24v infection and proved efficient in blocking HAdV-37 binding. Taken together, the pentavalent conjugates presented here form a basis for the development of general inhibitors of these highly contagious ocular pathogens.


  • Organizational Affiliation

    Department of Chemistry, Umeå University, SE90187 Umeå, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP1A [auth 111]305Coxsackievirus A24Mutation(s): 0 
UniProt
Find proteins for V9VEF3 (Coxsackievirus A24)
Explore V9VEF3 
Go to UniProtKB:  V9VEF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV9VEF3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP2B [auth 222]271Coxsackievirus A24Mutation(s): 0 
UniProt
Find proteins for V9VEF3 (Coxsackievirus A24)
Explore V9VEF3 
Go to UniProtKB:  V9VEF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV9VEF3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP3C [auth 333]240Coxsackievirus A24Mutation(s): 0 
UniProt
Find proteins for V9VEF3 (Coxsackievirus A24)
Explore V9VEF3 
Go to UniProtKB:  V9VEF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV9VEF3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP4D [auth 444]69Coxsackievirus A24Mutation(s): 0 
UniProt
Find proteins for V9VEF3 (Coxsackievirus A24)
Explore V9VEF3 
Go to UniProtKB:  V9VEF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV9VEF3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SIA (Subject of Investigation/LOI)
Query on SIA

Download Ideal Coordinates CCD File 
E [auth 111]N-acetyl-alpha-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
F [auth 111],
G [auth 111],
P [auth 222],
Q [auth 222]
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
J [auth 111],
K [auth 111],
L [auth 111],
R [auth 222],
V [auth 333]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth 111]
M [auth 111]
N [auth 111]
O [auth 111]
S [auth 222]
H [auth 111],
M [auth 111],
N [auth 111],
O [auth 111],
S [auth 222],
T [auth 333],
W [auth 333]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
U [auth 333]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth 111]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Work: 0.150 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 305.475α = 90
b = 365.351β = 90
c = 366.484γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyFOR2327
German Federal Ministry for Education and ResearchGermanyBW-Stiftung - Glykobiologie
Knut and Alice Wallenberg FoundationGermany2013.0019

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2022-11-09
    Changes: Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description