Native Influenza Neuraminidase in Complex with 4-amino-2-deoxy-2,3-dehydro-N-neuraminic Acid

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 

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This is version 2.0 of the entry. See complete history


Analysis of inhibitor binding in influenza virus neuraminidase.

Smith, B.J.Colman, P.M.Von Itzstein, M.Danylec, B.Varghese, J.N.

(2001) Protein Sci 10: 689-696

  • DOI: https://doi.org/10.1110/ps.41801
  • Primary Citation of Related Structures:  
    1F8B, 1F8C, 1F8D, 1F8E

  • PubMed Abstract: 

    2,3-didehydro-2-deoxy-N:-acetylneuraminic acid (DANA) is a transition state analog inhibitor of influenza virus neuraminidase (NA). Replacement of the hydroxyl at the C9 position in DANA and 4-amino-DANA with an amine group, with the intention of taking advantage of an increased electrostatic interaction with a conserved acidic group in the active site to improve inhibitor binding, significantly reduces the inhibitor activity of both compounds. The three-dimensional X-ray structure of the complexes of these ligands and NA was obtained to 1.4 A resolution and showed that both ligands bind isosterically to DANA. Analysis of the geometry of the ammonium at the C4 position indicates that Glu119 may be neutral when these ligands bind. A computational analysis of the binding energies indicates that the substitution is successful in increasing the energy of interaction; however, the gains that are made are not sufficient to overcome the energy that is required to desolvate that part of the ligand that comes in contact with the protein.

  • Organizational Affiliation

    Biomolecular Research Institute, Parkville, Victoria 3052, Australia. brian.smith@bioresi.com.au

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NEURAMINIDASE388Influenza A virus (A/tern/Australia/G70C/1975(H11N9))Mutation(s): 0 
Find proteins for P03472 (Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9))
Explore P03472 
Go to UniProtKB:  P03472
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03472
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G57082ZE
GlyCosmos:  G57082ZE
GlyGen:  G57082ZE
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
4AM PDBBind:  1F8C Ki: 40 (nM) from 1 assay(s)
Binding MOAD:  1F8C Ki: 40 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 
  • Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.98α = 90
b = 180.98β = 90
c = 180.98γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-11
    Type: Initial release
  • Version 1.1: 2008-01-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2015-03-11
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary