4D8S

Influenza NA in complex with antiviral compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/10.1021/jm301145k
  • Primary Citation of Related Structures:  
    4D8S

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuraminidase390Influenza A virus (A/duck/Ukraine/1/1963(H3N8))Mutation(s): 1 
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0HX
Query on 0HX

Download Ideal Coordinates CCD File 
C [auth A]pentan-3-yl 2-acetamido-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid
C13 H21 N O6
UUULUCUBSUJBNQ-UFGOTCBOSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
0HX Binding MOAD:  4D8S IC50: 320 (nM) from 1 assay(s)
PDBBind:  4D8S IC50: 320 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.192 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.388α = 90
b = 89.388β = 90
c = 94.754γ = 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: 2013-02-13
    Type: Initial release
  • Version 2.0: 2020-04-22
    Changes: Atomic model, Data collection, Database references, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary