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Journal of Computer-Aided Molecular Design

, Volume 21, Issue 9, pp 523–525 | Cite as

IA, database of known ligands of aminoacyl-tRNA synthetases

  • Mieczyslaw Torchala
  • Marcin Hoffmann
Article

Abstract

The IA database contains 240 structures of known inhibitors of aminoacyl-tRNA synthetases. Structures can be downloaded in different file formats (mol, sdf, smile, png). The search engine offers possibility of searching for the ligands with a given functional group. Additionally, one can search for ligands that act on selected synthetases and from particular references. The data include information which synthetase a given ligand inhibits together with the inhibition constant (IC50) if known. Database is freely available at http://ia.bioinfo.pl/

Keywords

Aminoacyl-tRNA synthetases Aminoacyl-tRNA synthetases inhibitors Molecular docking Virtual high throughput screening 

Notes

Acknowledgements

Financial support by European Commission and Polish Ministry for Education and Science is acknowledged (BioSapiens project grant number LSHG-CT-2003-503265, and grant number PBZ-MNiI-2/1/2005). MH thanks the Foundation for Polish Science for support via FOCUS program. The authors thank the anonymous referee for the suggestions on improving the IA database.

References

  1. 1.
    Szymanski M, Deniziak M, Barciszewski J (2000) Acta Biochim Pol 47:821Google Scholar
  2. 2.
    Pohlmann J, Brotz-Oesterhelt H (2004) Curr Drug Targets Infect Disord 4:261CrossRefGoogle Scholar
  3. 3.
    Kim S, Lee SW, Choi EC, Choi SY (2003) Appl Microbiol Biotechnol 61:278Google Scholar
  4. 4.
    Sukuru SCK, Crepin T, Milev Y, Marsh LC, Hill JB, Anderson RJ, Morris JC, Rohatgi A, O’Mahony G, Grøtli M, Danel F, Page MGP, Härtlein M, Cusack S, Kron MA, Kuhn LA (2006) J Comput Aided Mol Des 20:159CrossRefGoogle Scholar
  5. 5.
    Kim SE, Kim SY, Kim S, Kang T, Lee J (2005) Bioorg Med Chem Lett 15:3389CrossRefGoogle Scholar
  6. 6.
    Farhanullah, Kim SY, Yoon E-J, Choi E-C, Kim S, Kang T, Samrin F, Purie S, Lee J (2006) Bioorg Med Chem 14:7154CrossRefGoogle Scholar
  7. 7.
    Jarvest RL, Erskine SG, Forrest AK, Fosberry AP, Hibbs MJ, Jones JJ, O’Hanlon PJ, Sheppard RJ, Worby A (2005) Bioorg Med Chem Lett 15:2305CrossRefGoogle Scholar
  8. 8.
    Critchley IA, Young CL, Stone KC, Ochsner UA, Guiles J, Tarasow T, Janjic N (2005) Antimicrob Agents Chemother 49:4247CrossRefGoogle Scholar
  9. 9.
    Petraitis V, Petraitiene R, Kelaher AM, Sarafandi AA, Sein T, Mickiene D, Bacher J, Groll AH, Walsh TJ (2004) Antimicrob Agents Chemother 48:3959CrossRefGoogle Scholar
  10. 10.
    Kanamaru T, Nakano Y, Toyoda Y, Miyagawa KI, Tada M, Kaisho T, Nakao M (2001) Antimicrob Agents Chemother 45:2455CrossRefGoogle Scholar
  11. 11.
    Winum JY, Scozzafava A, Montero JL, Supuran CT (2005) Med Res Rev 25:186CrossRefGoogle Scholar
  12. 12.
    Schimmel P, Tao J, Hill J (1998) FASEB J 12:1599Google Scholar
  13. 13.
    Yu XY, Hill JM, Yu G, Yang Y, Kluge AF, Keith D, Finn J, Gallant P, Silverman J, Lim A (2001) Bioorg Med Chem Lett 11:541CrossRefGoogle Scholar
  14. 14.
    Banwell MG, Crasto CF, Easton CJ, Forrest AK, Karoli T, March DR, Mensah L, Nairn MR, O’Hanlon PJ, Oldham MD, Yue W (2000) Bioorg Med Chem Lett 10:2263CrossRefGoogle Scholar
  15. 15.
    Jarvest RL, Berge JM, Houge-Frydrych CS, Mensah LM, O’Hanlon PJ, Pope AJ (2001) Bioorg Med Chem Lett 11:2499CrossRefGoogle Scholar
  16. 16.
    Yu XY, Finn J, Hill JM, Wang ZG, Keith D, Silverman J, Oliver N (2004) Bioorg Med Chem Lett 14:1343CrossRefGoogle Scholar
  17. 17.
    Tandon M, Coffen DL, Gallant P, Keith D, Ashwell MA (2004) Bioorg Med Chem Lett 14:1909CrossRefGoogle Scholar
  18. 18.
    Hurdle JG, O’Neill AJ, Chopra I (2005) Antimicrob Agents Chemother 49:4821CrossRefGoogle Scholar
  19. 19.
    Jarvest RL, Armstrong SA, Berge JM, Brown P, Elder JS, Brown MJ, Copley RC, Forrest AK, Hamprecht DW, O’Hanlon PJ, Mitchell DJ, Rittenhouse S, Witty DR (2004) Bioorg Med Chem Lett 14:3937CrossRefGoogle Scholar
  20. 20.
    Jarvest RL, Berge JM, Brown P, Houge-Frydrych CS, O’Hanlon PJ, McNair DJ, Pope AJ, Rittenhouse S (2003) Bioorg Med Chem Lett 13:1265CrossRefGoogle Scholar
  21. 21.
    Qiu X, Janson CA, Smith WW, Green SM, McDevitt P, Johanson K, Carter P, Hibbs M, Lewis C, Chalker A, Fosberry A, Lalonde J, Berge J, Brown P, Houge-Frydrych CS, Jarvest RL (2001) Protein Sci 10:2008CrossRefGoogle Scholar
  22. 22.
    Finn J, Mattia K, Morytko M, Ram S, Yang Y, Wu X, Mak E, Gallant P, Keith D (2003) Bioorg Med Chem Lett 13:2231CrossRefGoogle Scholar
  23. 23.
    Lee J, Kim SE, Lee JY, Kim SY, Kang SU, Seo SH, Chun MW, Kang T, Choi SY, Kim HO (2003) Bioorg Med Chem Lett 13:1087CrossRefGoogle Scholar
  24. 24.
    Marvin applets. Retrieved from http://www.chemaxon.com/ 6/13/2007
  25. 25.
    Mayo SL, Olafson BD, Goddard WA III (1990) J Phys Chem 94:8897CrossRefGoogle Scholar
  26. 26.
    Moustakas DT, Lang PT, Pegg S, Pettersen E, Kuntz ID, Brooijmans N, Rizzo RC (2006) J Comput Aided Mol Des 20:601CrossRefGoogle Scholar
  27. 27.
    Bursulaya BD, Totrov M, Abagyan R, Brooks CL (2003) J Comput Aided Mol Des 17:755CrossRefGoogle Scholar
  28. 28.
    Eitner K, Gaweda T, Hoffmann M, Jura M, Rychlewski L, Barciszewski J (2007) J Chem Inf Model 47:695CrossRefGoogle Scholar
  29. 29.
    Zavodszky MI, Sanschagrin PC, Kuhn LA, Korde RS (2002) J Comput Aided Mol Des 16:883CrossRefGoogle Scholar
  30. 30.
    Sippl W (2002) J Comput Aided Mol Des 16:825CrossRefGoogle Scholar
  31. 31.
    Plewczynski D, Spieser SAH, Koch U (2006) J Chem Inf Model 46:1098CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  1. 1.BioInfoBank InstitutePoznanPoland
  2. 2.Faculty of PhysicsAdam Mickiewicz UniversityPoznanPoland
  3. 3.Faculty of ChemistryAdam Mickiewicz UniversityPoznanPoland

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