4PDW

A benzonitrile analogue inhibits rhinovirus replication

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 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
  • Primary Citation of Related Structures:  
    4PDW

  • 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).

    Organizational Affiliation: 

    Laboratory of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Genome polyprotein A289Rhinovirus B14Mutation(s): 0 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
Go to UniProtKB:  P03303
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Genome polyprotein B262Rhinovirus B14Mutation(s): 0 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
Go to UniProtKB:  P03303
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Genome polyprotein C236Rhinovirus B14Mutation(s): 0 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
Go to UniProtKB:  P03303
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein VP4/VP2 D68Rhinovirus BMutation(s): 0 
Find proteins for F5A5A0 (Rhinovirus B)
Explore F5A5A0 
Go to UniProtKB:  F5A5A0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2XK
Query on 2XK
Download Ideal Coordinates CCD File 
A
4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile
C17 H14 N2 O5
IDNLSCLFQWBBHS-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
A, B, C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 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
b = 439.411β = 90
c = 439.411γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
SCALAdata scaling
CNSrefinement
Cootmodel building
PHENIXmodel building

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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