1NA1

The structure of HRV14 when complexed with Pleconaril


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1128/JVI.78.20.11061-11069.2004
  • Primary Citation of Related Structures:  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 huma ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coat protein VP1
A
289Human rhinovirus 14EC: 3.6.1.15, 3.4.22.28, 3.4.22.29, 2.7.7.48
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coat protein VP2
B
262Human rhinovirus 14EC: 3.6.1.15, 3.4.22.28, 3.4.22.29, 2.7.7.48
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Coat protein VP3
C
236Human rhinovirus 14EC: 3.6.1.15, 3.4.22.28, 3.4.22.29, 2.7.7.48
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Coat protein VP4
D
68Human rhinovirus 14EC: 3.6.1.15, 3.4.22.28, 3.4.22.29, 2.7.7.48
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
W11
Query on W11

Download SDF File 
Download CCD File 
A
3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE
WIN63843
C18 H18 F3 N3 O3
KQOXLKOJHVFTRN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.222 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 437.160α = 90.00
b = 437.160β = 90.00
c = 437.160γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
ENVELOPEphasing
CCP4data scaling
ENVELOPEmodel building
DENZOdata reduction
TRUNCATEdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-16
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance