3CL0

N1 Neuraminidase H274Y + oseltamivir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants.

Collins, P.J.Haire, L.F.Lin, Y.P.Liu, J.Russell, R.J.Walker, P.A.Skehel, J.J.Martin, S.R.Hay, A.J.Gamblin, S.J.

(2008) Nature 453: 1258-1261

  • DOI: 10.1038/nature06956
  • Primary Citation of Related Structures:  
    3CKZ, 3CL0, 3CL2

  • PubMed Abstract: 
  • The potential impact of pandemic influenza makes effective measures to limit the spread and morbidity of virus infection a public health priority. Antiviral drugs are seen as essential requirements for control of initial influenza outbreaks caused by a new virus, and in pre-pandemic plans there is a heavy reliance on drug stockpiles ...

    The potential impact of pandemic influenza makes effective measures to limit the spread and morbidity of virus infection a public health priority. Antiviral drugs are seen as essential requirements for control of initial influenza outbreaks caused by a new virus, and in pre-pandemic plans there is a heavy reliance on drug stockpiles. The principal target for these drugs is a virus surface glycoprotein, neuraminidase, which facilitates the release of nascent virus and thus the spread of infection. Oseltamivir (Tamiflu) and zanamivir (Relenza) are two currently used neuraminidase inhibitors that were developed using knowledge of the enzyme structure. It has been proposed that the closer such inhibitors resemble the natural substrate, the less likely they are to select drug-resistant mutant viruses that retain viability. However, there have been reports of drug-resistant mutant selection in vitro and from infected humans. We report here the enzymatic properties and crystal structures of neuraminidase mutants from H5N1-infected patients that explain the molecular basis of resistance. Our results show that these mutants are resistant to oseltamivir but still strongly inhibited by zanamivir owing to an altered hydrophobic pocket in the active site of the enzyme required for oseltamivir binding. Together with recent reports of the viability and pathogenesis of H5N1 (ref. 7) and H1N1 (ref. 8) viruses with neuraminidases carrying these mutations, our results indicate that it would be prudent for pandemic stockpiles of oseltamivir to be augmented by additional antiviral drugs, including zanamivir.


    Organizational Affiliation

    MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NeuraminidaseA385Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 1 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for Q6DPL2 (Influenza A virus)
Explore Q6DPL2 
Go to UniProtKB:  Q6DPL2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G39
Query on G39

Download Ideal Coordinates CCD File 
B [auth A](3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid
C14 H24 N2 O4
NENPYTRHICXVCS-YNEHKIRRSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
G39IC50:  1   nM  BindingDB
G39IC50:  0.15000000596046448   nM  BindingDB
G39IC50:  1.2999999523162842   nM  BindingDB
G39IC50:  0.18000000715255737   nM  BindingDB
G39IC50:  4.5   nM  BindingDB
G39IC50:  7.099999904632568   nM  BindingDB
G39IC50:  5.400000095367432   nM  BindingDB
G39Ki:  1.100000023841858   nM  BindingDB
G39IC50:  3.299999952316284   nM  BindingDB
G39IC50:  0.11999999731779099   nM  BindingDB
G39IC50:  250   nM  BindingDB
G39IC50:  0.6000000238418579   nM  BindingDB
G39IC50:  1   nM  BindingDB
G39IC50:  0.10000000149011612   nM  BindingDB
G39IC50:  3.200000047683716   nM  BindingDB
G39IC50:  5.400000095367432   nM  BindingDB
G39IC50:  330   nM  BindingDB
G39IC50:  370   nM  BindingDB
G39Ki:  7.900000095367432   nM  BindingDB
G39IC50:  0.7300000190734863   nM  BindingDB
G39IC50:  7.099999904632568   nM  BindingDB
G39Ki:  4.900000095367432   nM  BindingDB
G39IC50:  0.30000001192092896   nM  BindingDB
G39IC50:  817   nM  BindingDB
G39Ki:  84.80000305175781   nM  Binding MOAD
G39IC50:  2.200000047683716   nM  BindingDB
G39Ki:  0.10000000149011612   nM  BindingDB
G39IC50:  2.9000000953674316   nM  BindingDB
G39IC50:  4.199999809265137   nM  BindingDB
G39IC50:  2.5999999046325684   nM  BindingDB
G39IC50:  11   nM  BindingDB
G39IC50:  100   nM  BindingDB
G39IC50:  0.4000000059604645   nM  BindingDB
G39IC50:  8.399999618530273   nM  BindingDB
G39IC50:  210   nM  BindingDB
G39IC50:  217   nM  BindingDB
G39IC50:  7.800000190734863   nM  BindingDB
G39IC50:  15   nM  BindingDB
G39IC50:  0.20000000298023224   nM  BindingDB
G39IC50:  16   nM  BindingDB
G39IC50:  0.4399999976158142   nM  BindingDB
G39Ki :  84.80000305175781   nM  PDBBind
G39IC50:  21   nM  BindingDB
G39IC50:  23   nM  BindingDB
G39IC50:  0.8999999761581421   nM  BindingDB
G39IC50:  26   nM  BindingDB
G39IC50:  1.7999999523162842   nM  BindingDB
G39IC50:  0.14000000059604645   nM  BindingDB
G39IC50:  0.17000000178813934   nM  BindingDB
G39IC50:  1   nM  BindingDB
G39IC50:  34   nM  BindingDB
G39IC50:  36   nM  BindingDB
G39IC50:  0.10000000149011612   nM  BindingDB
G39IC50:  2.0999999046325684   nM  BindingDB
G39IC50:  3.700000047683716   nM  BindingDB
G39IC50:  49   nM  BindingDB
G39IC50:  4.900000095367432   nM  BindingDB
G39IC50:  53   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.066α = 90
b = 115.066β = 90
c = 63.321γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2018-08-22
    Changes: Data collection, Database references, Source and taxonomy, Structure summary