1A4Q

INFLUENZA VIRUS B/BEIJING/1/87 NEURAMINIDASE COMPLEXED WITH DIHYDROPYRAN-PHENETHYL-PROPYL-CARBOXAMIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    1A4G, 1A4Q, 1BJI

  • 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 greater against influenza A enzyme ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NEURAMINIDASEA, B390Influenza B virus (STRAIN B/BEIJING/1/87)Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
Find proteins for P27907 (Influenza B virus (strain B/Beijing/1/1987))
Explore P27907 
Go to UniProtKB:  P27907
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DPC
Query on DPC

Download Ideal Coordinates CCD File 
E [auth A], I [auth B]5-ACETYLAMINO-4-AMINO-6-(PHENETHYL-PROPYL-CARBAMOYL)-5,6-DIHYDRO-4H-PYRAN-2-CARBOXYLIC ACID
C20 H27 N3 O5
ZNRGSYNQOLEMKF-CGTJXYLNSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A], G [auth B], H [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DPCIC50:  3600   nM  Binding MOAD
DPCIC50 :  3600   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.3α = 90
b = 88.3β = 90
c = 221.1γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data reduction
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-03-02
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary