4GB1

Synthesis and Evaluation of Novel 3-C-alkylated-Neu5Ac2en Derivatives as Probes of Influenza Virus Sialidase 150-loop flexibility


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Synthesis and evaluation of novel 3-C-alkylated-Neu5Ac2en derivatives as probes of influenza virus sialidase 150-loop flexibility.

Rudrawar, S.Kerry, P.S.Rameix-Welti, M.A.Maggioni, A.Dyason, J.C.Rose, F.J.van der Werf, S.Thomson, R.J.Naffakh, N.Russell, R.J.von Itzstein, M.

(2012) Org.Biomol.Chem. 10: 8628-8639

  • DOI: 10.1039/c2ob25627d

  • PubMed Abstract: 
  • Novel 3-C-alkylated-Neu5Ac2en derivatives have been designed to target the expanded active site cavity of influenza virus sialidases with an open 150-loop, currently seen in X-ray crystal structures of influenza A virus group-1 (N1, N4, N5, N8), but ...

    Novel 3-C-alkylated-Neu5Ac2en derivatives have been designed to target the expanded active site cavity of influenza virus sialidases with an open 150-loop, currently seen in X-ray crystal structures of influenza A virus group-1 (N1, N4, N5, N8), but not group-2 (N2, N9), sialidases. The compounds show selectivity for inhibition of H5N1 and pdm09 H1N1 sialidases over an N2 sialidase, providing evidence of the relative 150-loop flexibility of these sialidases. In a complex with N8 sialidase, the C3 substituent of 3-phenylally-Neu5Ac2en occupies the 150-cavity while the central ring and the remaining substituents bind the active site as seen for the unsubstituted template. This new class of inhibitors, which can 'trap' the open 150-loop form of the sialidase, should prove useful as probes of 150-loop flexibility.


    Organizational Affiliation

    Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland 4222, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neuraminidase
A
390Influenza A virus (strain A/Duck/Ukraine/1/1963 H3N8)Gene Names: NA
EC: 3.2.1.18
Find proteins for Q07599 (Influenza A virus (strain A/Duck/Ukraine/1/1963 H3N8))
Go to UniProtKB:  Q07599
Small Molecules
Ligands 2 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
0LP
Query on 0LP

Download SDF File 
Download CCD File 
A
5-(acetylamino)-2,6-anhydro-3,5-dideoxy-3-[(2E)-3-phenylprop-2-en-1-yl]-D-glycero-L-altro-non-2-enonic acid
C20 H25 N O8
LRXKGKMIXXSWGY-KXNCHKOWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.204 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 90.501α = 90.00
b = 90.501β = 90.00
c = 108.731γ = 90.00
Software Package:
Software NamePurpose
StructureStudiodata collection
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-26
    Type: Initial release
  • Version 1.1: 2012-10-31
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Structure summary