Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

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This is version 1.4 of the entry. See complete history


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: https://doi.org/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. 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
390Influenza B virus (STRAIN B/BEIJING/1/87)Mutation(s): 0 
Find proteins for P27907 (Influenza B virus (strain B/Beijing/1/1987))
Explore P27907 
Go to UniProtKB:  P27907
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27907
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
ZMR Binding MOAD:  1A4G IC50: 4 (nM) from 1 assay(s)
PDBBind:  1A4G IC50: 4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.2α = 90
b = 88.2β = 90
c = 221.1γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data reduction
X-PLORmodel building
CCP4data scaling

Structure Validation

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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
  • Version 1.4: 2023-08-02
    Changes: Database references, Refinement description, Structure summary