4D8S

Influenza NA in complex with antiviral compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.398 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Exploring the interactions of unsaturated glucuronides with influenza virus sialidase.

Bhatt, B.Bohm, R.Kerry, P.S.Dyason, J.C.Russell, R.J.Thomson, R.J.von Itzstein, M.

(2012) J.Med.Chem. 55: 8963-8968

  • DOI: 10.1021/jm301145k

  • PubMed Abstract: 
  • A series of C3 O-functionalized 2-acetamido-2-deoxy-Δ⁴-β-D-glucuronides were synthesized to explore noncharge interactions in subsite 2 of the influenza virus sialidase active site. In complex with A/N8 sialidase, the parent compound (C3 OH) inverts ...

    A series of C3 O-functionalized 2-acetamido-2-deoxy-Δ⁴-β-D-glucuronides were synthesized to explore noncharge interactions in subsite 2 of the influenza virus sialidase active site. In complex with A/N8 sialidase, the parent compound (C3 OH) inverts its solution conformation to bind with all substituents well positioned in the active site. The parent compound inhibits influenza virus sialidase at a sub-μM level; the introduction of small alkyl substituents or an acetyl group at C3 is also tolerated.


    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
0HX
Query on 0HX

Download SDF File 
Download CCD File 
A
pentan-3-yl 2-(acetylamino)-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid
C13 H21 N O6
UUULUCUBSUJBNQ-UFGOTCBOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0HXIC50: 320 nM BINDINGMOAD
0HXIC50: 320 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.398 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 89.388α = 90.00
b = 89.388β = 90.00
c = 94.754γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release