1VCJ

Influenza B virus neuraminidase complexed with 1-(4-Carboxy-2-(3-pentylamino)phenyl)-5-aminomethyl-5-hydroxymethyl-pyrrolidin-2-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A benzoic acid inhibitor induces a novel conformational change in the active site of Influenza B virus neuraminidase.

Lommer, B.S.Ali, S.M.Bajpai, S.N.Brouillette, W.J.Air, G.M.Luo, M.

(2004) Acta Crystallogr.,Sect.D 60: 1017-1023

  • DOI: 10.1107/S0907444904006225

  • PubMed Abstract: 
  • Owing to the highly conserved nature of its active site, Influenza B virus neuraminidase (NA) has emerged as a major target for the design of novel anti-influenza drugs. A benzene-ring scaffold has been used in place of the pyranose ring of sialic ac ...

    Owing to the highly conserved nature of its active site, Influenza B virus neuraminidase (NA) has emerged as a major target for the design of novel anti-influenza drugs. A benzene-ring scaffold has been used in place of the pyranose ring of sialic acid to develop simpler NA inhibitors that contain a minimal number of chiral centers. A new compound belonging to this series, BANA 207, showed significant improvement in inhibitory activity against Influenza B virus NA compared with its parent compound. Here, the structural analysis of a complex of BANA 207 with influenza virus B/Lee/40 NA is reported. The results indicate that BANA 207 forms an unexpected interaction with the crucial active-site residue Glu275 that stabilizes the side chain of this residue in a conformation previously unobserved in NA-inhibitor complexes. This change in the side-chain orientation of Glu275 alters the topology of the triglycerol pocket, which accommodates an additional lipophilic substitution at the benzene ring and may provide an explanation for the increased activity of BANA 207 against Influenza B virus NA.


    Organizational Affiliation

    Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEURAMINIDASE
A
389Influenza B virus (strain B/Lee/1940)Gene Names: NA
EC: 3.2.1.18
Find proteins for P03474 (Influenza B virus (strain B/Lee/1940))
Go to UniProtKB:  P03474
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IBA
Query on IBA

Download SDF File 
Download CCD File 
A
4-[(2R)-2-(AMINOMETHYL)-2-(HYDROXYMETHYL)-5-OXOPYRROLIDIN-1-YL]-3-[(1-ETHYLPROPYL)AMINO]BENZOIC ACID
1-(4-CARBOXY-2-(3-PENTYLAMINO)PHENYL)-5-AMINOMETHYL-5-HYDROXYMETHYL-PYRROLIDIN-2-ONE
C18 H27 N3 O4
ZEZFFRWWHKSMEB-GOSISDBHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IBAIC50: 26000 nM BINDINGMOAD
IBAIC50: 26000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.214 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 124.360α = 90.00
b = 124.360β = 90.00
c = 71.470γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
SAINTdata scaling
SADIEdata collection
SAINTdata reduction
X-PLORphasing
SADIEdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2011-10-05
    Type: Derived calculations