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: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

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Ligand Structure Quality Assessment 


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 D Biol Crystallogr 60: 1017-1023

  • DOI: 10.1107/S0907444904006225
  • Primary Citation of Related Structures:  
    1VCJ

  • 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 acid to develop simpler NA inhibitors that contain a minimal number of chiral centers ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NEURAMINIDASEA389Influenza B virus (B/Lee/1940)Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for P03474 (Influenza B virus (strain B/Lee/1940))
Explore P03474 
Go to UniProtKB:  P03474
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IBA (Subject of Investigation/LOI)
Query on IBA

Download Ideal Coordinates CCD File 
B [auth A]4-[(2R)-2-(AMINOMETHYL)-2-(HYDROXYMETHYL)-5-OXOPYRROLIDIN-1-YL]-3-[(1-ETHYLPROPYL)AMINO]BENZOIC ACID
C18 H27 N3 O4
ZEZFFRWWHKSMEB-GOSISDBHSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
IBA Binding MOAD:  1VCJ IC50: 2.60e+4 (nM) from 1 assay(s)
PDBBind:  1VCJ IC50: 2.60e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.36α = 90
b = 124.36β = 90
c = 71.47γ = 90
Software Package:
Software NamePurpose
SADIEdata collection
SAINTdata reduction
X-PLORmodel building
X-PLORrefinement
SADIEdata reduction
SAINTdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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