2QWG

THE X-RAY STRUCTURE OF A COMPLEX OF 5-N-ACETYL-4-AMINO-6-DIETHYLCARBOXAMIDE-4,5-DIHYDRO-2H-PYRAN-2-CARBOXYLIC ACID AND A DRUG RESISTANT VARIANT R292K OF TERN N9 INFLUENZA VIRUS NEURAMINIDASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

wwPDB Validation 3D Report Full Report



Literature

Drug design against a shifting target: a structural basis for resistance to inhibitors in a variant of influenza virus neuraminidase.

Varghese, J.N.Smith, P.W.Sollis, S.L.Blick, T.J.Sahasrabudhe, A.McKimm-Breschkin, J.L.Colman, P.M.

(1998) Structure 6: 735-746

  • DOI: 10.1016/s0969-2126(98)00075-6
  • Primary Citation of Related Structures:  
    2QWK, 2QWJ, 2QWI, 2QWH, 2QWG, 2QWF, 2QWE, 2QWD, 2QWC, 2QWB

  • PubMed Abstract: 
  • Inhibitors of the influenza virus neuraminidase have been shown to be effective antiviral agents in humans. Several studies have reported the selection of novel influenza strains when the virus is cultured with neuraminidase inhibitors in vitro. Thes ...

    Inhibitors of the influenza virus neuraminidase have been shown to be effective antiviral agents in humans. Several studies have reported the selection of novel influenza strains when the virus is cultured with neuraminidase inhibitors in vitro. These resistant viruses have mutations either in the neuraminidase or in the viral haemagglutinin. Inhibitors in which the glycerol sidechain at position 6 of 2-deoxy-2,3-dehydro-N-acetylneuraminic acid (Neu5Ac2en) has been replaced by carboxamide-linked hydrophobic substituents have recently been reported and shown to select neuraminidase variants. This study seeks to clarify the structural and functional consequences of replacing the glycerol sidechain of the inhibitor with other chemical constituents.


    Related Citations: 
    • Mutations in a Conserved Residue in the Influenza Virus Neuraminidase Active Site Decreases Sensitivity to Neu5Ac2En-Derived Inhibitors
      Mckimm-Breschkin, J.L., Sahasrabudhe, A., Blick, T.J., Mcdonald, M., Colman, P.M., Hart, G.J., Bethell, R.C., Varghese, J.N.
      (1998) J Virol 72: 2456

    Organizational Affiliation

    Biomolecular Research Institute 343 Royal Parade, Parkville, 3052, Australia. jose.varghese@bioresi.com.au



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NEURAMINIDASEA388Influenza A virusMutation(s): 1 
EC: 3.2.1.18
Find proteins for P03472 (Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9))
Explore P03472 
Go to UniProtKB:  P03472
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
7 N-Glycosylation Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G28
Query on G28

Download CCD File 
A
5-N-acetyl-4-amino-6-diethyl carboxamide-4,5-dihydro-2H-pyran-2-carboxylic acid
C13 H21 N3 O5
YQUCNOUQEZHVSC-JMJZKYOTSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
G28IC50:  230000   nM  Binding MOAD
G28IC50 :  230000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.89α = 90
b = 180.89β = 90
c = 180.89γ = 90
Software Package:
Software NamePurpose
R-AXISIIdata collection
PROTEINdata reduction
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
PROTEINdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1998-04-07 
  • Released Date: 1998-11-11 
  • Deposition Author(s): Varghese, J.N.

Revision History 

  • Version 1.0: 1998-11-11
    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
  • Version 2.0: 2020-04-22
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary