4PDW

A benzonitrile analogue inhibits rhinovirus replication


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A novel benzonitrile analogue inhibits rhinovirus replication.

Lacroix, C.Querol-Audi, J.Roche, M.Franco, D.Froeyen, M.Guerra, P.Terme, T.Vanelle, P.Verdaguer, N.Neyts, J.Leyssen, P.

(2014) J.Antimicrob.Chemother. 69: 2723-2732

  • DOI: 10.1093/jac/dku200

  • PubMed Abstract: 
  • To study the characteristics and the mode of action of the anti-rhinovirus compound 4-[1-hydroxy-2-(4,5-dimethoxy-2-nitrophenyl)ethyl]benzonitrile (LPCRW_0005).

    To study the characteristics and the mode of action of the anti-rhinovirus compound 4-[1-hydroxy-2-(4,5-dimethoxy-2-nitrophenyl)ethyl]benzonitrile (LPCRW_0005).


    Organizational Affiliation

    Laboratory of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.,Aix-Marseille Université, Institut de Chimie Radicalaire UMR 7273 CNRS 27, Boulevard Jean Moulin, Marseille, France.,Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.,Laboratory of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium johan.neyts@rega.kuleuven.be.,Molecular Biology Institute of Barcelona (IBMB), Consejo Superior de Investigaciones Científicas, Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Genome polyprotein
A
289Human rhinovirus 14Mutation(s): 0 
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Genome polyprotein
B
262Human rhinovirus 14Mutation(s): 0 
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Genome polyprotein
C
236Human rhinovirus 14Mutation(s): 0 
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP4/VP2
D
68Rhinovirus BMutation(s): 0 
Find proteins for F5A5A0 (Rhinovirus B)
Go to UniProtKB:  F5A5A0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
2XK
Query on 2XK

Download SDF File 
Download CCD File 
A
4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile
C17 H14 N2 O5
IDNLSCLFQWBBHS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.200 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 439.411α = 90.00
b = 439.411β = 90.00
c = 439.411γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
Cootmodel building
PHENIXmodel building
SCALAdata scaling
XDSdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-09-24
    Type: Database references