5NZF

Complex of H275Y/I223V mutant variant of neuraminidase from H1N1 influenza virus with oseltamivir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus.

Pokorna, J.Pachl, P.Karlukova, E.Hejdanek, J.Rezacova, P.Machara, A.Hudlicky, J.Konvalinka, J.Kozisek, M.

(2018) Viruses 10

  • DOI: https://doi.org/10.3390/v10070339
  • Primary Citation of Related Structures:  
    5NWE, 5NZ4, 5NZE, 5NZF, 5NZN

  • PubMed Abstract: 

    Neuraminidase is the main target for current influenza drugs. Reduced susceptibility to oseltamivir, the most widely prescribed neuraminidase inhibitor, has been repeatedly reported. The resistance substitutions I223V and S247N, alone or in combination with the major oseltamivir-resistance mutation H275Y, have been observed in 2009 pandemic H1N1 viruses. We overexpressed and purified the ectodomain of wild-type neuraminidase from the A/California/07/2009 (H1N1) influenza virus, as well as variants containing H275Y, I223V, and S247N single mutations and H275Y/I223V and H275Y/S247N double mutations. We performed enzymological and thermodynamic analyses and structurally examined the resistance mechanism. Our results reveal that the I223V or S247N substitution alone confers only a moderate reduction in oseltamivir affinity. In contrast, the major oseltamivir resistance mutation H275Y causes a significant decrease in the enzyme’s ability to bind this drug. Combination of H275Y with an I223V or S247N mutation results in extreme impairment of oseltamivir’s inhibition potency. Our structural analyses revealed that the H275Y substitution has a major effect on the oseltamivir binding pose within the active site while the influence of other studied mutations is much less prominent. Our crystal structures also helped explain the augmenting effect on resistance of combining H275Y with both substitutions.


  • Organizational Affiliation

    The Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry, Flemingovo n. 2, 166 10 Prague 6, Czech Republic. jana.pokorna@uochb.cas.cz.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuraminidase
A, B, C, D
388unidentified influenza virusMutation(s): 0 
Gene Names: NA
UniProt
Find proteins for C3W6G3 (Influenza A virus)
Explore C3W6G3 
Go to UniProtKB:  C3W6G3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3W6G3
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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
E
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G39
Query on G39

Download Ideal Coordinates CCD File 
EA [auth D],
I [auth A],
O [auth B],
X [auth C]
(3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid
C14 H24 N2 O4
NENPYTRHICXVCS-YNEHKIRRSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
FA [auth D]
GA [auth D]
J [auth A]
K [auth A]
P [auth B]
FA [auth D],
GA [auth D],
J [auth A],
K [auth A],
P [auth B],
Q [auth B],
R [auth B],
Y [auth C],
Z [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
HA [auth D]
IA [auth D]
JA [auth D]
AA [auth C],
BA [auth C],
HA [auth D],
IA [auth D],
JA [auth D],
KA [auth D],
LA [auth D],
MA [auth D],
S [auth B],
T [auth B],
U [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth D]
DA [auth D]
G [auth A]
H [auth A]
L [auth A]
CA [auth D],
DA [auth D],
G [auth A],
H [auth A],
L [auth A],
M [auth B],
N [auth B],
V [auth C],
W [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
NA [auth D]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
G39 Binding MOAD:  5NZF Ki: 9.40e+4 (nM) from 1 assay(s)
BindingDB:  5NZF Ki: min: 0.1, max: 10 (nM) from 5 assay(s)
IC50: min: 0.1, max: 210 (nM) from 17 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.654α = 90
b = 127.217β = 92.93
c = 96.786γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary