The binding of 3′-N-piperidine-4-carboxyl-3′-deoxy-ara-uridine to ribonuclease A in the crystal

Bioorganic and Medicinal Chemistry

Volumn 14, Issue 17, 2006, Pages 6055-6064

  Leonidas, Demetres D ^a   Maiti, Tushar Kanti ^b   Samanta, Anirban ^b   Dasgupta, Swagata ^b   Pathak, Tanmaya ^b   Zographos, Spyros E ^a   Oikonomakos, Nikos G ^a  

^a INSTITUTE OF BIOLOGY   (Greece)

^b INDIAN INSTITUTE OF TECHNOLOGY   (India)

Author keywords

2 fluoro 2 deoxyuridine 3 phosphate; 3 N Piperidine 4 carboxyl 3 deoxy ara uridine; 3 N piperidine 4 carboxyl 3 deoxy ara uridine; 3e; 5 phospho 2 deoxyuridine 3 pyrophosphate (P 5 ) adenosine 3 phosphate; arabinouridine 3 phosphate; araUMP; bovine pancreatic ribonuclease A; deoxyuridine 3 phosphate; dUFMP; dUMP; inhibition; pdUppA 3 p; PEG; poly(ethylene glycol); Ribonuclease A; RNase A; Structure assisted inhibitor design; X ray crystallography

Indexed keywords

CARBOXYL GROUP; PIPERIDINE DERIVATIVE; RIBONUCLEASE A; URIDINE; 3' N PIPERIDINE 4 CARBOXYL 3' DEOXY ARA URIDINE; 3'-N-PIPERIDINE-4-CARBOXYL-3'-DEOXY-ARA-URIDINE; DRUG DERIVATIVE; PANCREATIC RIBONUCLEASE;

ARTICLE; CRYSTAL STRUCTURE; DRUG DETERMINATION; DRUG POTENCY; DRUG PROTEIN BINDING; DRUG STRUCTURE; ENZYME ACTIVE SITE; LIGAND BINDING; MOLECULAR RECOGNITION; PROTEIN LOCALIZATION; RNA BINDING; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; PROTEIN BINDING;

ARA;

BINDING SITES; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PIPERIDINES; PROTEIN BINDING; RIBONUCLEASE, PANCREATIC; URIDINE;

EID: 33746042950     PISSN: 09680896     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bmc.2006.05.011     Document Type: Article

References (55)

1. Cho S., Beintema J.J., and Zhang J. Genomics 85 (2005) 208
2. Cho S., and Zhang J. Gene (2006)
3. Loverix S., and Steyaert J. Curr. Med. Chem. 10 (2003) 779
4. Riordan J.F. Methods Enzymol. 341 (2001) 263
5. Rosenberg H.F., and Domachowske J.B. J. Leukocyte Biol. 70 (2001) 691
6. Rosenberg H.F., and Domachowske J.B. Methods Enzymol. 341 (2001) 273
7. Venge P., Bystrom J., Carlson M., Hakansson L., Karawacjzyk M., Peterson C., Seveus L., and Trulson A. Clin. Exp. Allergy 29 (1999) 1172
8. Russo A., Acharya K.R., and Shapiro R. Methods Enymol. 341 (2001) 629
9. Jenkins J.L., Kao R.Y., and Shapiro R. Proteins 50 (2003) 81
10. Jenkins J.L., and Shapiro R. Biochemistry 43 (2003) 6674
11. Beintema J.J., and Kleineidam R.G. Cell. Mol. Life Sci. 54 (1998) 825
12. Raines R.T. Chem. Rev. 98 (1998) 1045
13. Leonidas D.D., Chavali G.B., Oikonomakos N.G., Chrysina E.D., Kosmopoulou M.N., Vlassi M., Frankling C., and Acharya K.R. Protein Sci. 12 (2003) 2559
14. Jenkins C.L., Thiyagarajan N., Sweeney R.Y., Guy M.P., Kelemen B.R., Acharya K.R., and Raines R.T. FEBS J. 272 (2005) 744
15. Leonidas D.D., Shapiro R., Irons L.I., Russo N., and Acharya K.R. Biochemistry 38 (1999) 10287
16. Russo N., and Shapiro R. J. Biol. Chem. 274 (1999) 14902
17. Maiti T.K., Soumya D., Dasgupta S., and Pathak T. Bioorg. Med. Chem. 14 (2006) 1221
18. Leonidas D.D., Shapiro R., Irons L.I., Russo N., and Acharya K.R. Biochemistry 36 (1997) 5578
19. Hatzopoulos G.N., Leonidas D.D., Kardakaris R., Kobe J., and Oikonomakos N.G. FEBS J. 272 (2005) 3988
20. Borkakoti N., Moss D.A., and Palmer R.A. Acta Crystallogr. B38 (1982) 2210
21. Howlin B., Moss D.S., and Harris G.W. Acta Crystallogr. A45 (1989) 851
22. deMel V.S.J., Doscher M.S., Martin P.D., and Edwards B.F.P. FEBS Lett. 349 (1994) 155
23. Mazzarella L., Capasso S., Demasi D., Di'Lorenzo G., Mattia C.A., and Zagari A. Acta Crystallogr. D49 (1993) 389
24. Berisio R., Lamzin V.S., Sica F., Wilson K.S., Zagari A., and Mazzarella L. J. Mol. Biol. 292 (1999) 845
25. Fedorov A.A., Joseph-McCarthy D., Fedorov E., Sirakova D., Graf I., and Almo S.C. Biochemistry 35 (1996) 15962
26. Borkakoti N. Eur. J. Biochem. 132 (1983) 89
27. Moodie S.L., and Thornton J.M. Nucleic Acids Res. 21 (1993) 1369
28. Witzel H., and Barnard E.A. Biochem. Biophys. Res. Commun. 7 (1962) 295
29. McPherson A., Brayer G.D., and Morrison R.D. J. Mol. Biol. 189 (1986) 305
30. Zegers I., Maes D., Dao-Thi M.-H., Poortmans F., Palmer R., and Wyns L. Protein Sci. 31 (1994) 2322
31. Toiron C., Gonzalez C., Bruix M., and Rico M. Protein Sci. 5 (1996) 1633
32. Richards F.M., Wyckoff H.W., and Ribonuclease S. In: Philips D.C., and Richards F.M. (Eds). Atlas of Molecular Structures in Biology Vol. 1 (1973), Clarendon, Oxford, UK
33. Gilliland G.L., Dill J., Pechik I., Svensson L.A., and Sjolin L. Protein Pept. Lett. 1 (1994) 60
34. Wodak S.Y., Liu M.Y., and Wyckoff H.W. J. Mol. Biol. 116 (1977) 855
35. Fontecilla-Camps J.C., de Llorens R., le Du M.H., and Cuchillo C.M. J. Biol. Chem. 269 (1994) 21526
36. Jardine A.M., Leonidas D.D., Jenkins J.L., Park C., Raines R.T., Acharya K.R., and Shapiro R. Biochemistry 40 (2001) 10262
37. Schultz L.W., Quirk D.J., and Raines R.T. Biochemistry 37 (1998) 8886
38. Lawrence M.C., and Colman P.M. J. Mol. Biol. 234 (1993) 946
39. Anderson D.G., Hammes G.G., and Walz F.G. Biochemistry 7 (1968) 1637
40. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. In: Carter C.W.J., and Sweet R.M. (Eds). Methods in Enzymology Vol. 276 (1997), Academic Press, New York 307
41. French S., and Wilson K.S. Acta Crystallogr. A34 (1978) 517
42. Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Acta Crystallogr. A47 (1991) 110
43. Murshudov G.N., Vagin A.A., and Dodson E.J. Acta Crystallogr. D53 (1997) 240
44. Painter J., and Merritt E.A. J. Appl. Crystallogr. 39 (2005) 109
45. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. J. Appl. Crystallogr. 26 (1993) 283
46. Hubbard, S. J.; Thornton, J. M. NACCESS, Computer Program, Department of Biochemistry and Molecular Biology, University College London, 1993.
47. Kraulis P.J. J. Appl. Crystallogr. 24 (1991) 946
48. Esnouf R.M. J. Mol. Graphics Model. 15 (1997) 132
49. Merritt E.A., and Bacon D.J. Macromol. Crystallogr. B277 (1997) 505
50. Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., and Olson A.J. J. Comput. Chem. 19 (1998) 1639
51. IUPAC-IUB, Eur. J. Biochem. 1983, 131, 9.
52. Altona C., and Sundaralingam M. J. Am. Chem. Soc. 94 (1972) 8205
53. McDonald I.K., and Thornton J.M. J. Mol. Biol. 238 (1994) 777
54. Brünger A.T. Nature 355 (1992) 472
55. Nicholls A., and Honig B. J. Comput. Chem. 12 (1991) 435