Sequence and structural analysis of kinase ATP pocket residues

Farmaco

Volumn 59, Issue 10, 2004, Pages 759-765

  Vulpetti, Anna ^a   Bosotti, Roberta ^b  

^a Viale Pasteur 10 20014 N ^*  (Italy)

^b Alfa Biotech   (Italy)

Author keywords

ATP pocket; Protein kinase; Sequence analysis; Structural analysis

Indexed keywords

ADENOSINE TRIPHOSPHATE; PHOSPHOTRANSFERASE; PHOSPHOTRANSFERASE INHIBITOR;

AMINO ACID SEQUENCE; ARTICLE; DRUG DESIGN; DRUG SPECIFICITY; ENZYME ANALYSIS; ENZYME BINDING; ENZYME STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

ADENOSINE TRIPHOSPHATE; AMINO ACID SEQUENCE; BINDING SITES; DRUG DESIGN; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; PROTEIN KINASES; SEQUENCE ALIGNMENT;

EID: 5044236233     PISSN: 0014827X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.farmac.2004.05.010     Document Type: Article

References (33)

1. Manning G., Whyte D.B., Martinez R., Hunter T., and Sudarsanam S. The protein kinase complement of the human genome Science 298 2002 1912 1934
2. Toledo L.M., Lydon N.B., and Elbaum D. The structure-based design of ATP-site directed protein kinase inhibitors Curr Med Chem. 9 1999 775 805
3. Wang Z., Canagarajah B.J., Boehm J.C., Kassisa S., Cobb M.H., Young P.R., Abdel-Meguid S., Adams J.L., and Goldsmith E.J. Structural basis of inhibitor selectivity in MAP kinases Structure 6 1998 1117 1128
4. Schindler T., Sicheri F., Pico A., Gazit A., Levitzki A., and Kuriyan J. Crystal structure of Hck in complex with a Src family-selective tyrosine kinase inhibitor Mol. Cell. 3 1999 639 648
5. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The Protein Data Bank Nucleic Acids Res. 28 2000 235 242
6. Eddy S.R. Profile hidden Markov models Bioinformatics 14 1998 755 763
7. Pierce A.C., Sandretto K.L., and Bemis G.W. Kinase inhibitors and the case for CH...O hydrogen bonds in protein-ligand binding Proteins 49 2002 567 576
8. Toledo L.M., and Lydon N.B. Structures of staurosporine bound to CDK2 and cAPK-new tools for structure-based design of protein kinase inhibitors Structure 5 1997 1551 1556
9. Zhu X., Kim J.L., Newcomb J.R., Rose P.E., Stover D.R., Toledo L.M., Zhao H., and Morgenstern K.A. Structural analysis of the lymphocyte-specific kinase Lck in complex with non-selective and Src family selective kinase inhibitors Structure. Fold. Des. 7 1999 651 661
10. Lamers M.B., Antson A.A., Hubbard R.E., Scott R.K., and Williams D.H. Structure of the protein tyrosine kinase domain of C-terminal Src kinase (CSK) in complex with staurosporine J. Mol. Biol. 285 1999 713 725
11. Zhao B., Bower M.J., McDevitt P.J., Zhao H., Davis S.T., Johanson K.O., Green S.M., Concha N.O., and Zhou B.S. Structural Basis for Chk1 inhibition by UCN-01 J. Biol. Chem. 277 2002 46609 46615
12. Komander D., Kular G.S., Bain J., Elliott M., Alessi D.R., and Van Aalten D.M. Structural basis for UCN-01 (7-hydroxystaurosporine) specificity and PDK1 (3-phosphoinositide-dependent protein kinase-1) inhibition Biochem. J. 375 2003 255 262
13. Longenecker K.L., Roach P.J., and Hurley T.D. Three-dimensional structure of mammalian casein kinase I: molecular basis for phosphate recognition J. Mol. Biol. 257 1996 618 631
14. Stahura F.L., Xue L., Godden J.W., and Bajorath J. Molecular scaffold-based design and comparison of combinatorial libraries focused on the ATP-binding site of protein kinases J. Mol. Graph. Model. 17 1999 1 9
15. Mao L., Wang Y., Liu Y., and Hu X. Molecular determinants for ATP-binding in proteins: a data mining and quantum chemical analysis J. Mol. Biol. 336 2004 787 807
16. Denessiouk K.A., and Johnson M.S. When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families Proteins 38 2000 310 326
17. Traxler P.M., Furet P., Mett H., Buchdunger E., Meyer T., and Lydon N. 4-(Phenylamino)pyrrolopyrimidines: potent and selective, ATP site directed inhibitors of the EGF-receptor protein tyrosine kinase J. Med. Chem. 39 1996 2285 2292
18. Palmer B.D., Trumpp-Kallmeyer S., Fry D.W., Nelson J.M., Showalter H.D., and Denny W.A. Tyrosine kinase inhibitors. 11. Soluble analogues of pyrrolo- and pyrazoloquinazolines as epidermal growth factor receptor inhibitors: synthesis, biological evaluation, and modeling of the mode of binding J. Med. Chem. 40 1997 1519 1529
19. Wissner A., Overbeek E., Reich M.F., Floyd M.B., Johnson B.D., Mamuya N., Rosfjord E.C., Discafani C., Davis R., Shi X., Rabindran S.K., Gruber B.C., Ye F., Hallett W.A., Nilakantan R., Shen R., Wang Y.F., Greenberger L.M., and Tsou H.R. Synthesis and structure-activity relationships of 6,7-disubstituted 4-anilinoquinoline-3-carbonitriles. The design of an orally active, irreversible inhibitor of the tyrosine kinase activity of the epidermal growth factor receptor (EGFR) and the human epidermal growth factor receptor-2 (HER-2) J. Med. Chem. 46 2003 49 63
20. Pargellis C., Tong L., Churchill L., Cirillo P.F., Gilmore T., Graham A.G., Grob P.M., Hickey E.R., Moss N., Pav S., and Regan J. Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site Nat. Struct. Biol. 9 2002 268 272
21. Schindler T., Bornmann W., Pellicena P., Miller W.T., Clarkson B., and Kuriyan J. Structural mechanism for STI-571 inhibition of abelson tyrosine kinase Science 289 2000 1938 1942
22. Eyers P.A., Craxton M., Morrice N., Cohen P., and Goedert M. Conversion of SB 203580-insensitive MAP kinase family members to drug-sensitive forms by a single amino-acid substitution Chem. Biol. 5 1998 321 328
23. Mohammadi M., Froum S., Hamby J.M., Schroeder M.C., Panek R.L., Lu G.H., Eliseenkova A.V., Green D., Schlessinger J., and Hubbard S.R. Crystal structure of an angiogenesis inhibitor bound to the FGF receptor tyrosine kinase domain EMBO J. 17 1998 5896 5904
24. Kraybill B.C., Elkin L.L., Blethrow J.D., Morgan D.O., and Shokat K.M. Inhibitor scaffolds as new allele specific kinase substrates J. Am. Chem. Soc. 124 2002 12118 12128
25. Kong N., Fotouhi N., Wovkulich P.M., and Roberts J. Drugs Future 28 2003 881 896
26. Cramer R.D. III, Patterson D.E., and Bunce J.D. Recent advances in comparative molecular field analysis (CoMFA) Prog. Clin. Biol. Res. 291 1989 161 165
27. Klebe G., Abraham U., and Mietzner T. Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity J. Med. Chem. 37 1994 4130 4146
28. Klebe G., and Abraham U. Comparative molecular similarity index analysis (CoMSIA) to study hydrogen-bonding properties and to score combinatorial libraries J. Comput. Aided Mol. Des. 13 1999 1 10
29. Bohm M., Strzebecher J., and Klebe G. Three-dimensional quantitative structure-activity relationship analyses using comparative molecular field analysis and comparative molecular similarity indices analysis to elucidate selectivity differences of inhibitors binding to trypsin, thrombin, and factor Xa J. Med. Chem. 42 1999 458 477
30. Myshkin E., and Wang B. Chemometrical classification of ephrin ligands and Eph kinases using GRID/CPCA approach J. Chem. Inf. Comput. Sci. 43 2003 1004 1010
31. Terp G.E., Cruciani G., Christensen I.T., and Jorgensen F.S. Structural differences of matrix metalloproteinases with potential implications for inhibitor selectivity examined by the GRID/CPCA approach J. Med. Chem. 45 2002 2675 2684
32. Kastenholz M.A., Pastor M., Cruciani G., Haaksma E.E., and Fox T. GRID/CPCA: a new computational tool to design selective ligands J. Med. Chem. 43 2000 3033 3044
33. Sheridan R.P., Holloway M.K., McGaughey G., Mosley R.T., and Singh S.B. A simple method for visualizing the differences between related receptor sites J. Mol. Graph. Model. 21 2002 217 225