1ND3

The structure of HRV16, when complexed with pleconaril, an antiviral compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and virological studies of the stages of virus replication that are affected by antirhinovirus compounds

Zhang, Y.Simpson, A.A.Ledford, R.M.Bator, C.M.Chakravarty, S.Skochko, G.A.Demenczuk, T.M.Watanyar, A.Pevear, D.C.Rossmann, M.G.

(2004) J Virol 78: 11061-11069

  • DOI: https://doi.org/10.1128/JVI.78.20.11061-11069.2004
  • Primary Citation of Related Structures:  
    1NA1, 1NCQ, 1NCR, 1ND2, 1ND3

  • PubMed Abstract: 

    Pleconaril is a broad-spectrum antirhinovirus and antienterovirus compound that binds into a hydrophobic pocket within viral protein 1, stabilizing the capsid and resulting in the inhibition of cell attachment and RNA uncoating. When crystals of human rhinovirus 16 (HRV16) and HRV14 are incubated with pleconaril, drug occupancy in the binding pocket is lower than when pleconaril is introduced during assembly prior to crystallization. This effect is far more marked in HRV16 than in HRV14 and is more marked with pleconaril than with other compounds. These observations are consistent with virus yield inhibition studies and radiolabeled drug binding studies showing that the antiviral effect of pleconaril against HRV16 is greater on the infectivity of progeny virions than the parent input viruses. These data suggest that drug integration into the binding pocket during assembly, or at some other late stage in virus replication, may contribute to the antiviral activity of capsid binding compounds.


  • Organizational Affiliation

    Department of Biological Sciences, Lilly Hall, Purdue University, 915 W. State St., West Lafayette, IN 47907-2054, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
coat protein VP1285rhinovirus A16Mutation(s): 0 
UniProt
Find proteins for Q82122 (Human rhinovirus 16)
Explore Q82122 
Go to UniProtKB:  Q82122
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ82122
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
coat protein VP2261rhinovirus A16Mutation(s): 0 
UniProt
Find proteins for Q82122 (Human rhinovirus 16)
Explore Q82122 
Go to UniProtKB:  Q82122
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ82122
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
coat protein VP3238rhinovirus A16Mutation(s): 0 
UniProt
Find proteins for Q82122 (Human rhinovirus 16)
Explore Q82122 
Go to UniProtKB:  Q82122
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ82122
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
coat protein VP468rhinovirus A16Mutation(s): 0 
UniProt
Find proteins for Q82122 (Human rhinovirus 16)
Explore Q82122 
Go to UniProtKB:  Q82122
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ82122
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
W11
Query on W11

Download Ideal Coordinates CCD File 
F [auth A]3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE
C18 H18 F3 N3 O3
KQOXLKOJHVFTRN-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 360.301α = 90
b = 343.331β = 90
c = 332.632γ = 90

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-16
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations