1QJY

HUMAN RHINOVIRUS 16 COAT PROTEIN IN COMPLEX WITH ANTIVIRAL COMPOUND VP65099


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.3 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.USA 96: 14730

  • DOI: 10.1073/pnas.96.26.14730
  • Primary Citation of Related Structures:  

  • 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 v ...

    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.


    Related Citations: 
    • The Refined Structure of Human Rhinovirus 16 at 2.15 Angstroms Resolution: Implications for the Viral Life Cycle
      Hadfield, A.T.,Lee, W.M.,Zhao, R.,Oliveira, M.A.,Minor, I.,Rueckert, R.R.,Rossmann, M.G.
      (1997) Structure 5: 427
    • The Site of Attachment in Human Rhinovirus 14 for Antiviral Agents that Inhibit Uncoating
      Smith, T.J.,Kremer, M.J.,Luo, M.,Vriend, G.,Arnold, E.,Kamer, G.,Rossmann, M.G.,Mckinlay, M.A.,Diana, G.D.,Otto, M.J.
      (1986) Science 233: 1286
    • A Comparison of the Anti-Rhinoviral Drug Binding Pocket in Hrv14 and Hrv1A
      Kim, K.H.,Willingmann, P.,Gong, Z.X.,Kremer, M.J.,Chapman, M.S.,Minor, I.,Oliveira, M.A.,Rossmann, M.G.,Andries, K.,Diana, G.D.,Dutko, F.J.,Mckinlay, M.A.,Pevear, D.C.
      (1993) J.Mol.Biol. 230: 206
    • Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses
      Rossmann, M.G.,Arnold, E.,Erickson, J.W.,Frankenberger, E.A.,Griffith, J.P.,Hecht, H.J.,Johnson, J.E.,Kamer, G.,Luo, M.,Mosser, A.G.,Rueckert, R.R.,Sherry, B.,Vriend, G.
      (1985) Nature 317: 145
    • Crystal Structure of Human Rhinovirus Serotype 1A (Hrv1A)
      Kim, S.S.,Smith, T.J.,Chapman, M.S.,Rossmann, M.G.,Pevear, D.C.,Dutko, F.J.,Felock, P.J.,Diana, G.D.,Mckinlay, M.A.
      (1989) J.Mol.Biol. 210: 91
    • The Structure of Human Rhinovirus 16
      Oliveira, M.A.,Zhao, R.,Lee, W.M.,Kremer, M.J.,Minor, I.,Rueckert, R.R.,Diana, G.D.,Pevear, D.C.,Dutko, F.J.,Mckinlay, M.A.,Rossmann, M.G.
      (1993) Structure 1: 51


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN VP1
1
285Human rhinovirus 16Mutation(s): 0 
Find proteins for Q82122 (Human rhinovirus 16)
Go to UniProtKB:  Q82122
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN VP2
2
261Human rhinovirus 16Mutation(s): 0 
Find proteins for Q82122 (Human rhinovirus 16)
Go to UniProtKB:  Q82122
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN VP3
3
238Human rhinovirus 16Mutation(s): 0 
Find proteins for Q82122 (Human rhinovirus 16)
Go to UniProtKB:  Q82122
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PROTEIN VP4
4
68Human rhinovirus 16Mutation(s): 0 
Find proteins for Q82122 (Human rhinovirus 16)
Go to UniProtKB:  Q82122
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download SDF File 
Download CCD File 
4
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
1
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
W03
Query on W03

Download SDF File 
Download CCD File 
1
2,6-DIMETHYL-1-(3-[3-METHYL-5-ISOXAZOLYL]-PROPANYL)-4-[2-METHYL-4-ISOXAZOLYL]-PHENOL
WIN65099
C19 H22 N2 O3
SLPKYEWAKMNCPT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.233 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 362.600α = 90.00
b = 347.100β = 90.00
c = 334.900γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
PURDUEdata reduction
X-PLORrefinement
PURDUEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-07-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-05-08
    Type: Data collection, Derived calculations, Experimental preparation, Other