3O9K

Influenza NA in complex with compound 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 
    0.296 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Novel sialic acid derivatives lock open the 150-loop of an influenza A virus group-1 sialidase.

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

(2010) Nat Commun 1: 113-113

  • DOI: https://doi.org/10.1038/ncomms1114
  • Primary Citation of Related Structures:  
    3O9J, 3O9K

  • PubMed Abstract: 

    Influenza virus sialidase has an essential role in the virus' life cycle. Two distinct groups of influenza A virus sialidases have been established, that differ in the flexibility of the '150-loop', providing a more open active site in the apo form of the group-1 compared to group-2 enzymes. In this study we show, through a multidisciplinary approach, that novel sialic acid-based derivatives can exploit this structural difference and selectively inhibit the activity of group-1 sialidases. We also demonstrate that group-1 sialidases from drug-resistant mutant influenza viruses are sensitive to these designed compounds. Moreover, we have determined, by protein X-ray crystallography, that these inhibitors lock open the group-1 sialidase flexible 150-loop, in agreement with our molecular modelling prediction. This is the first direct proof that compounds may be developed to selectively target the pandemic A/H1N1, avian A/H5N1 and other group-1 sialidase-containing viruses, based on an open 150-loop conformation of the enzyme.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuraminidase387Influenza A virus (A/duck/Ukraine/1/1963(H3N8))Mutation(s): 0 
EC: 3.2.1.18
UniProt
Find proteins for Q07599 (Influenza A virus (strain A/Duck/Ukraine/1/1963 H3N8))
Explore Q07599 
Go to UniProtKB:  Q07599
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07599
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ETT
Query on ETT

Download Ideal Coordinates CCD File 
B [auth A]5-acetamido-2,6-anhydro-3,5-dideoxy-3-[(2E)-3-(4-methylphenyl)prop-2-en-1-yl]-D-glycero-D-galacto-non-2-enonic acid
C21 H27 N O8
CCPSTGRFUHTVNN-ZSEVYCOTSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free:  0.296 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.491α = 90
b = 90.491β = 90
c = 107.778γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-04-22
    Changes: Advisory, Atomic model, Data collection, Database references, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 2.2: 2024-11-06
    Changes: Data collection, Database references, Structure summary