1INW

A SIALIC ACID DERIVED PHOSPHONATE ANALOG INHIBITS DIFFERENT STRAINS OF INFLUENZA VIRUS NEURAMINIDASE WITH DIFFERENT EFFICIENCIES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A sialic acid-derived phosphonate analog inhibits different strains of influenza virus neuraminidase with different efficiencies.

White, C.L.Janakiraman, M.N.Laver, W.G.Philippon, C.Vasella, A.Air, G.M.Luo, M.

(1995) J Mol Biol 245: 623-634

  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A phosphonate analog of N-acetyl neuraminic acid (PANA) has been designed as a potential neuraminidase (NA) inhibitor and synthesized as both the alpha (ePANA) and beta (aPANA) anomers. Inhibition of type A (N2) and type B NA activity by ePANA was ap ...

    A phosphonate analog of N-acetyl neuraminic acid (PANA) has been designed as a potential neuraminidase (NA) inhibitor and synthesized as both the alpha (ePANA) and beta (aPANA) anomers. Inhibition of type A (N2) and type B NA activity by ePANA was approximately a 100-fold better than by sialic acid, but inhibition of type A (N9) NA was only ten-fold better than by sialic acid. The aPANA compound was not a strong inhibitor for any of the NA strains tested. The crystal structures at 2.4 A resolution of ePANA complexed to type A (N2) NA, type A (N9) NA and type B NA and aPANA complexed to type A (N2) NA showed that neither of the PANA compounds distorted the NA active site upon binding. No significant differences in the NA-ePANA complex structures were found to explain the anomalous inhibition of N9 neuraminidase by ePANA. We put forward the hypothesis that an increase in the ePANA inhibition compared to that caused by sialic acid is due to (1) a stronger electrostatic interaction between the inhibitor phosphonyl group and the active site arginine pocket and (2) a lower distortion energy requirement for binding of ePANA.


    Related Citations: 
    • Structure of Influenza Virus Neuraminidase B(Slash)Lee(Slash)40 Complexed with Sialic Acid and a Dehydro Analog at 1.8 Angstroms Resolution: Implications for the Catalytic Mechanism
      Janakiraman, M.N., White, C.L., Laver, W.G., Air, G.M., Luo, M.
      (1994) Biochemistry 33: 8172
    • Three-Dimensional Structure of the Influenza Virus A(Slash)Tokyo(Slash)3(Slash)67 at 2.2 Angstroms Resolution
      Varghese, J.N., Colman, P.M.
      (1991) J Mol Biol 221: 473
    • Refined Atomic Structures of N9 Subtype Influenza Virus Neuraminidase and Escape Mutants
      Lip, W.R., Varghese, J.N., Baker, A.T., Van Danelaar, A., Laver, W.G., Webster, R.G., Colman, P.M.
      (1991) J Mol Biol 221: 487
    • Phosphonic-Acid Analogs of the N-Acetyl-2-Deoxyneuraminic Acids: Synthesis and Inhibition of Vibrio Choleae Sialidase
      Walliman, K., Vasella, A.
      (1990) Helv Chim Acta 73: 1359

    Organizational Affiliation

    Center for Macromolecular Crystallography, University of Alabama at Birmingham 35294.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INFLUENZA A SUBTYPE N2 NEURAMINIDASE
A
388Influenza A virusMutation(s): 0 
EC: 3.2.1.18
Find proteins for P06820 (Influenza A virus (strain A/Tokyo/3/1967 H2N2))
Go to UniProtKB:  P06820
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AXP
Query on AXP

Download CCD File 
A
4-ACETAMIDO-2,4-DIDEXOY-D-GLYCERO-BETA-D-GALACTO-OCTOPYRANOSYLPHOSPHONIC ACID (AN AXIAL PHOSPHONATE)
C10 H20 N O9 P
QITAGYVZDNZULE-HDBWYCHPSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MAN
Query on MAN

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

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.08α = 90
b = 141.67β = 90
c = 141.87γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-02-07
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance