Crystal structure of 2009 pandemic H1N1 neuraminidase complexed with oseltamivir

Experimental Data Snapshot

  • Resolution: 1.69 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 

Starting Model: experimental
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Structural and functional analysis of laninamivir and its octanoate prodrug reveals group specific mechanisms for influenza NA inhibition

Vavricka, C.J.Li, Q.Wu, Y.Qi, J.Wang, M.Liu, Y.Gao, F.Liu, J.Feng, E.He, J.Wang, J.Liu, H.Jiang, H.Gao, G.F.

(2011) PLoS Pathog 7: e1002249-e1002249

  • DOI: https://doi.org/10.1371/journal.ppat.1002249
  • Primary Citation of Related Structures:  
    3TI3, 3TI4, 3TI5, 3TI6, 3TI8, 3TIA, 3TIB, 3TIC

  • PubMed Abstract: 

    The 2009 H1N1 influenza pandemic (pH1N1) led to record sales of neuraminidase (NA) inhibitors, which has contributed significantly to the recent increase in oseltamivir-resistant viruses. Therefore, development and careful evaluation of novel NA inhibitors is of great interest. Recently, a highly potent NA inhibitor, laninamivir, has been approved for use in Japan. Laninamivir is effective using a single inhaled dose via its octanoate prodrug (CS-8958) and has been demonstrated to be effective against oseltamivir-resistant NA in vitro. However, effectiveness of laninamivir octanoate prodrug against oseltamivir-resistant influenza infection in adults has not been demonstrated. NA is classified into 2 groups based upon phylogenetic analysis and it is becoming clear that each group has some distinct structural features. Recently, we found that pH1N1 N1 NA (p09N1) is an atypical group 1 NA with some group 2-like features in its active site (lack of a 150-cavity). Furthermore, it has been reported that certain oseltamivir-resistant substitutions in the NA active site are group 1 specific. In order to comprehensively evaluate the effectiveness of laninamivir, we utilized recombinant N5 (typical group 1), p09N1 (atypical group 1) and N2 from the 1957 pandemic H2N2 (p57N2) (typical group 2) to carry out in vitro inhibition assays. We found that laninamivir and its octanoate prodrug display group specific preferences to different influenza NAs and provide the structural basis of their specific action based upon their novel complex crystal structures. Our results indicate that laninamivir and zanamivir are more effective against group 1 NA with a 150-cavity than group 2 NA with no 150-cavity. Furthermore, we have found that the laninamivir octanoate prodrug has a unique binding mode in p09N1 that is different from that of group 2 p57N2, but with some similarities to NA-oseltamivir binding, which provides additional insight into group specific differences of oseltamivir binding and resistance.

  • Organizational Affiliation

    CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
388Influenza A virus (A/California/04/2009(H1N1))Mutation(s): 0 
Gene Names: NA
Find proteins for C3W5S3 (Influenza A virus (strain swl A/California/04/2009 H1N1))
Explore C3W5S3 
Go to UniProtKB:  C3W5S3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3W5S3
Glycosylation Sites: 2
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on G39

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

Download Ideal Coordinates CCD File 
D [auth A],
N [auth B],
O [auth B],
P [auth B]
C8 H15 N O6
Query on GOL

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I [auth A],
L [auth A],
T [auth B]
C3 H8 O3
Query on ACT

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J [auth A]
K [auth A]
M [auth A]
U [auth B]
V [auth B]
J [auth A],
K [auth A],
M [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
C2 H3 O2
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
Q [auth B],
R [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
G39 BindingDB:  3TI6 Ki: min: 0.1, max: 10 (nM) from 5 assay(s)
IC50: min: 0.1, max: 210 (nM) from 20 assay(s)
PDBBind:  3TI6 IC50: 0.54 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.69 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.236α = 90
b = 137.157β = 90
c = 118.654γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-23
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary