Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design


The worldwide spread of H5N1 avian influenza has raised concerns that this virus might acquire the ability to pass readily among humans and cause a pandemic. Two anti-influenza drugs currently being used to treat infected patients are oseltamivir (Tamiflu) and zanamivir (Relenza), both of which target the neuraminidase enzyme of the virus. Reports of the emergence of drug resistance make the development of new anti-influenza molecules a priority. Neuraminidases from influenza type A viruses form two genetically distinct groups: group-1 contains the N1 neuraminidase of the H5N1 avian virus and group-2 contains the N2 and N9 enzymes used for the structure-based design of current drugs. Here we show by X-ray crystallography that these two groups are structurally distinct. Group-1 neuraminidases contain a cavity adjacent to their active sites that closes on ligand binding. Our analysis suggests that it may be possible to exploit the size and location of the group-1 cavity to develop new anti-influenza drugs.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it


Prices may be subject to local taxes which are calculated during checkout

Figure 1: Genetic and structural relationships between neuraminidases from different influenza viruses.
Figure 2: Molecular surfaces of group-1 and group-2 neuraminidases with bound oseltamivir showing the 150-cavity in the group-1 structure that arises because of the distinct conformation of the 150-loop.
Figure 3: Oseltamivir binding to the active sites of group-1 neuraminidases.
Figure 4: Locations of the oseltamivir resistance mutations found in group-1 and group-2 neuraminidases.


  1. Murphy, B. R. & Webster, R. G. in Fields Virology 3rd edn (eds Fields, D. B. N., Knipe, M. & Howley, P. M.) 1397–1445 (Lippincott-Raven, Philadelphia, 1996)

    Google Scholar 

  2. World Health Organization. A revision of the system of nomenclature for influenza viruses: a WHO memorandum. Bull. World Health Organ. 58, 585–591 (1980)

    Google Scholar 

  3. Bender, C. et al. Characterization of the surface proteins of influenza A (H5N1) viruses isolated from humans in 1997–1998. Virology 254, 115–123 (1999)

    Article  CAS  PubMed  Google Scholar 

  4. World Health Organization Global Influenza Program Surveillance Network. Evolution of H5N1 avian influenza viruses in Asia. Emerg. Infect. Dis. 11, 1515–1521 (2005)

    Article  Google Scholar 

  5. Thompson, J. D., Higgins, D. G. & Gibson, T. J. Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput. Appl. Biosci. 10, 19–29 (1994)

    CAS  PubMed  Google Scholar 

  6. von Itzstein, M. et al. Rational design of potent sialidase-based inhibitors of influenza virus replication. Nature 363, 418–423 (1993)

    Article  ADS  CAS  PubMed  Google Scholar 

  7. Kim, C. U. et al. Influenza neuraminidase inhibitors possessing a novel hydrophobic interaction in the enzyme active site: design, synthesis, and structural analysis of carbocyclic sialic acid analogues with potent anti-influenza activity. J. Am. Chem. Soc. 119, 681–690 (1997)

    Article  CAS  PubMed  Google Scholar 

  8. Varghese, J. N., Laver, W. G. & Colman, P. M. Structure of the influenza virus glycoprotein antigen neuraminidase at 2.9 Å resolution. Nature 303, 35–40 (1983)

    Article  ADS  CAS  Google Scholar 

  9. Baker, A. T., Varghese, J. N., Laver, W. G., Air, G. M. & Colman, P. M. Three-dimensional structure of neuraminidase of subtype N9 from an avian influenza virus. Proteins 2, 111–117 (1987)

    Article  CAS  PubMed  Google Scholar 

  10. Burmeister, W. P., Ruigrok, R. W. & Cusack, S. The 2.2 Å resolution crystal structure of influenza B neuraminidase and its complex with sialic acid. EMBO J. 11, 49–56 (1992)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Ives, J. et al. Anti-viral drug resistance: an oseltamivir treatment-selected influenza A/N2 virus with a R292K mutation in the neuraminidase gene has reduced infectivity in vivo. J. Clin. Virol. 18, 251–269 (2000)

    Article  Google Scholar 

  12. Gubareva, L. V., Kaiser, L., Matrosovich, M. N., Soo-Hoo, Y. & Hayden, F. G. Selection of influenza virus mutants in experimentally infected volunteers treated with oseltamivir. J. Infect. Dis. 183, 523–531 (2001)

    Article  CAS  Google Scholar 

  13. Carr, J. et al. Influenza virus carrying neuraminidase with reduced sensitivity to oseltamivir carboxylate has altered properties in vitro and is compromised for infectivity and replicative ability in vivo. Antiviral Res. 54, 79–88 (2002)

    Article  CAS  PubMed  Google Scholar 

  14. Ward, P., Small, I., Smith, J., Suter, P. & Dutkowski, R. Oseltamivir (Tamiflu) and its potential for use in the event of an influenza pandemic. J. Antimicrob. Chemother. 55 (suppl. 1), i5–i21 (2005)

    Article  CAS  PubMed  Google Scholar 

  15. Brouillette, W. J. et al. Pyrrolidinobenzoic acid inhibitors of influenza virus neuraminidase: modifications of essential pyrrolidinone ring substituents. Bioorg. Med. Chem. 11, 2739–2749 (2003)

    Article  CAS  PubMed  Google Scholar 

  16. Webster, R. G., Peiris, M., Chen, H. & Guan, Y. H5N1 outbreaks and enzootic influenza. Emerg. Infect. Dis. 12, 3–8 (2006)

    Article  PubMed  PubMed Central  Google Scholar 

  17. Colman, P. M., Varghese, J. N. & Laver, W. G. Structure of the catalytic and antigenic sites in influenza virus neuraminidase. Nature 303, 41–44 (1983)

    Article  ADS  CAS  Google Scholar 

  18. Bossart-Whitaker, P. et al. Three-dimensional structure of influenza A N9 neuraminidase and its complex with the inhibitor 2-deoxy 2,3-dehydro-N-acetyl neuraminic acid. J. Mol. Biol. 232, 1069–1083 (1993)

    Article  CAS  PubMed  Google Scholar 

  19. Burmeister, W. P., Henrissat, B., Bosso, C., Cusack, S. & Ruigrok, R. W. Influenza B virus neuraminidase can synthesize its own inhibitor. Structure 1, 19–26 (1993)

    Article  CAS  PubMed  Google Scholar 

  20. Meindl, P., Bodo, G., Palese, P., Schulman, J. & Tuppy, H. Inhibition of neuraminidase activity by derivatives of 2-deoxy-2,3-dehydro-N-acetylneuraminic acid. Virology 58, 457–463 (1974)

    Article  CAS  PubMed  Google Scholar 

  21. Babu, Y. S. et al. BCX-1812 (RWJ-270201): discovery of a novel, highly potent, orally active, and selective influenza neuraminidase inhibitor through structure-based drug design. J. Med. Chem. 43, 3482–3486 (2000)

    Article  CAS  PubMed  Google Scholar 

  22. Mishin, V. P., Hayden, F. G. & Gubareva, L. V. Susceptibilities of antiviral-resistant influenza viruses to novel neuraminidase inhibitors. Antimicrob. Agents Chemother. 49, 4515–4520 (2005)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Wang, M. Z., Tai, C. Y. & Mendel, D. B. Mechanism by which mutations at His 274 alter sensitivity of influenza A virus N1 neuraminidase to oseltamivir carboxylate and zanamivir. Antimicrob. Agents Chemother. 46, 3809–3816 (2002)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Yen, H. L. et al. Neuraminidase inhibitor-resistant influenza viruses may differ substantially in fitness and transmissibility. Antimicrob. Agents Chemother. 49, 4075–4084 (2005)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Varghese, J. N. et al. Drug design against a shifting target: a structural basis for resistance to inhibitors in a variant of influenza virus neuraminidase. Structure 6, 735–746 (1998)

    Article  CAS  PubMed  Google Scholar 

  26. Le, Q. M. et al. Avian flu: isolation of drug-resistant H5N1 virus. Nature 437, 1108 (2005)

    Article  ADS  CAS  PubMed  Google Scholar 

  27. Kiso, M. et al. Resistant influenza A viruses in children treated with oseltamivir: descriptive study. Lancet 364, 759–765 (2004)

    Article  CAS  PubMed  Google Scholar 

  28. de Jong, M. D. et al. Oseltamivir resistance during treatment of influenza A (H5N1) infection. N. Engl. J. Med. 353, 2667–2672 (2005)

    Article  ADS  CAS  PubMed  Google Scholar 

  29. Crawford, P. C. et al. Transmission of equine influenza virus to dogs. Science 310, 482–485 (2005)

    Article  ADS  CAS  PubMed  Google Scholar 

  30. Ha, Y., Stevens, D. J., Skehel, J. J. & Wiley, D. C. X-ray structures of H5 avian and H9 swine influenza virus hemagglutinins bound to avian and human receptor analogs. Proc. Natl Acad. Sci. USA 98, 11181–11186 (2001)

    Article  ADS  CAS  PubMed  Google Scholar 

  31. Otwinowski, Z. & Minor, W. in Data Collection and Processing (eds Sawyer, L., Isaacs, N. & Bailey, S.) 556–562 (SERC Daresbury Laboratory, Warrington, 1993)

    Google Scholar 

  32. CCP4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D 50, 760–763 (1994)

    Article  Google Scholar 

  33. Brunger, A. T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)

    Article  CAS  Google Scholar 

  34. Jones, T. A., Zhou, J. Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991)

    Article  Google Scholar 

Download references


This work was supported by the MRC (UK) and by an International Partnership Research Award in Veterinary Epidemiology from the Wellcome Trust. R.J.R. acknowledges the Wellcome Trust and the University of St Andrews for support and Biocryst for supply of peramivir. We thank P. Walker for assistance with data collection and preparation of the manuscript, and Rigaku (Europe) and CRUK (Lincoln's Inn) for access to data collection facilities.

Author information

Authors and Affiliations


Corresponding author

Correspondence to John J. Skehel.

Ethics declarations

Competing interests

Coordinates have been deposited with the Protein Data Bank and the relevant accession codes (2HTY, 2HU0, 2HU4, 2HT5, 2HTR, 2HT7, 2HT8, 2HTQ, 2HTU, 2HTV and 2HTW) are described in Supplementary Table 1. Reprints and permissions information is available at The authors declare no competing financial interests.

Supplementary information

Supplementary Figure 1

Comparison of the superposed active sites of Influenza B neuraminidase with that of the Influenza N9 neuraminidase. (JPG 74 kb)

Supplementary Figure 2

The ‘open’ structure of N1 with bound oseltamivir. (JPG 109 kb)

Supplementary Figure 3

Binding of DANA, Zanamivir, and Peramivir neuraminidase inhibitors to the active sites of Group-1 and Group-2 NAs. (JPG 51 kb)

Supplementary Notes

This file contains Supplementary Table 1 and Supplementary Figure Legends. (DOC 47 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Russell, R., Haire, L., Stevens, D. et al. The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design. Nature 443, 45–49 (2006).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing