1F8D

Native Influenza Neuraminidase in Complex with 9-amino-2-deoxy-2,3-dehydro-N-neuraminic Acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1110/ps.41801
  • Primary Citation of Related Structures:  

  • 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 tak ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEURAMINIDASE
A
388Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9)Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
Find proteins for P03472 (Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9))
Go to UniProtKB:  P03472
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
9AM
Query on 9AM

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Download CCD File 
A
9-AMINO-2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
C11 H18 N2 O7
VJTPBNUXDULDQD-UFGQHTETSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9AMKi: 400000 nM BINDINGMOAD
9AMKi: 400000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 
  • Space Group: I 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 180.740α = 90.00
b = 180.740β = 90.00
c = 180.740γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
SCALEPACKdata scaling
DENZOdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-11
    Type: Initial release
  • Version 1.1: 2008-01-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2015-03-11
    Type: Other