1QJY

HUMAN RHINOVIRUS 16 COAT PROTEIN IN COMPLEX WITH ANTIVIRAL COMPOUND VP65099


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Analysis of Three Structurally Related Antiviral Compounds in Complex with Human Rhinovirus 16

Hadfield, A.T.Minor, I.Diana, G.D.Rossmann, M.G.

(1999) Proc Natl Acad Sci U S A 96: 14730

  • DOI: https://doi.org/10.1073/pnas.96.26.14730
  • Primary Citation of Related Structures:  
    1QJU, 1QJX, 1QJY

  • PubMed Abstract: 

    Rhinoviruses are a frequent cause of the common cold. A series of antirhinoviral compounds have been developed that bind into a hydrophobic pocket in the viral capsid, stabilizing the capsid and interfering with cell attachment. The structures of a variety of such compounds, complexed with rhinovirus serotypes 14, 16, 1A, and 3, previously have been examined. Three chemically similar compounds, closely related to a drug that is undergoing phase III clinical trials, were chosen to determine the structural impact of the heteroatoms in one of the three rings. The compounds were found to have binding modes that depend on their electronic distribution. In the compound with the lowest efficacy, the terminal ring is displaced by 1 A and rotated by 180 degrees relative to the structure of the other two. The greater polarity of the terminal ring in one of the three compounds leads to a small displacement of its position relative to the other compounds in the hydrophobic end of the antiviral compound binding pocket to a site where it makes fewer interactions. Its lower efficacy is likely to be the result of the reduced number of interactions. A region of conserved residues has been identified near the entrance to the binding pocket where there is a corresponding conservation of the mode of binding of these compounds to different serotypes. Thus, variations in residues lining the more hydrophobic end of the pocket are primarily responsible for the differences in drug efficacies.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN VP1A [auth 1]285rhinovirus 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
PROTEIN VP2B [auth 2]261rhinovirus 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
PROTEIN VP3C [auth 3]238rhinovirus 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
PROTEIN VP4D [auth 4]68rhinovirus 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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
W03
Query on W03

Download Ideal Coordinates CCD File 
F [auth 1]2,6-DIMETHYL-1-(3-[3-METHYL-5-ISOXAZOLYL]-PROPANYL)-4-[2-METHYL-4-ISOXAZOLYL]-PHENOL
C19 H22 N2 O3
SLPKYEWAKMNCPT-UHFFFAOYSA-N
MYR
Query on MYR

Download Ideal Coordinates CCD File 
G [auth 4]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth 1]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 362.6α = 90
b = 347.1β = 90
c = 334.9γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
PURDUEdata reduction
PURDUEdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-07-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description