1A4G

INFLUENZA VIRUS B/BEIJING/1/87 NEURAMINIDASE COMPLEXED WITH ZANAMIVIR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dihydropyrancarboxamides related to zanamivir: a new series of inhibitors of influenza virus sialidases. 2. Crystallographic and molecular modeling study of complexes of 4-amino-4H-pyran-6-carboxamides and sialidase from influenza virus types A and B.

Taylor, N.R.Cleasby, A.Singh, O.Skarzynski, T.Wonacott, A.J.Smith, P.W.Sollis, S.L.Howes, P.D.Cherry, P.C.Bethell, R.Colman, P.Varghese, J.

(1998) J.Med.Chem. 41: 798-807

  • DOI: 10.1021/jm9703754
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The first paper in this series (see previous article) described structure-activity studies of carboxamide analogues of zanamivir binding to influenza virus sialidase types A and B and showed that inhibitory activity of these compounds was much greate ...

    The first paper in this series (see previous article) described structure-activity studies of carboxamide analogues of zanamivir binding to influenza virus sialidase types A and B and showed that inhibitory activity of these compounds was much greater against influenza A enzyme. To understand the large differences in affinities, a number of protein-ligand complexes have been investigated using crystallography and molecular dynamics. The crystallographic studies show that the binding of ligands containing tertiary amide groups is accompanied by the formation of an intramolecular planar salt bridge between two amino acid residues in the active site of the enzyme. It is proposed that the unexpected strong binding of these inhibitors is a result of the burial of hydrophobic surface area and salt-bridge formation in an environment of low dielectric. In sialidase from type A virus, binding of the carboxamide moeity and salt-bridge formation have only a minor effect on the positions of the surrounding residues, whereas in type B enzyme, significant distortion of the protein is observed. The results suggest that the decreased affinity in enzyme from influenza B is directly correlated with the small changes that occur in the amino acid residue interactions accompanying ligand binding. Molecular dynamics calculations have shown that the tendency for salt-bridge formation is greater in influenza A sialidase than influenza B sialidase and that this tendency is a useful descriptor for the prediction of inhibitor potency.


    Related Citations: 
    • The 2.2 A Resolution Crystal Structure of Influenza B Neuraminidase and its Complex with Sialic Acid
      Burmeister, W.P.,Ruigrok, R.W.,Cusack, S.
      (1992) Embo J. 11: 49
    • Sequence and Crystallization of Influenza Virus B/Beijing/1/87 Neuraminidase
      Burmeister, W.P.,Daniels, R.S.,Dayan, S.,Gagnon, J.,Cusack, S.,Ruigrok, R.W.
      (1991) Virology 180: 266


    Organizational Affiliation

    Department of Biomolecular Structure, Glaxo Wellcome Research and Development Limited, Hertfordshire, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEURAMINIDASE
A, B
390Influenza B virus (strain B/Beijing/1/1987)Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
Find proteins for P27907 (Influenza B virus (strain B/Beijing/1/1987))
Go to UniProtKB:  P27907
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
ZMR
Query on ZMR

Download SDF File 
Download CCD File 
A, B
ZANAMIVIR
MODIFIED SIALIC ACID
C12 H20 N4 O7
ARAIBEBZBOPLMB-UFGQHTETSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZMRKi: 0.1 nM (94) BINDINGDB
ZMRIC50: 1.7 - 20 nM (94) BINDINGDB
ZMRIC50: 4 nM BINDINGMOAD
ZMRIC50: 4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.198 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.200α = 90.00
b = 88.200β = 90.00
c = 221.100γ = 120.00
Software Package:
Software NamePurpose
CCP4data scaling
CCP4data reduction
X-PLORrefinement
X-PLORmodel building
X-PLORphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-03-02
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance