Primary Citation PubMed: 12169624
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Conservation, variability and the modeling of active protein kinases.
(2007) PLoS One 2
PubMed: 17912359 | PubMedCentral: PMC1989141 | DOI: 10.1371/journal.pone.0000982
When compared against the partially active-conformation structure of PDK1 (PDB code: 1H1W,  ), the top ranked prediction had 198 of 285 side chains positioned within 2 Å of... their actual location, a C α RMSD of 1.3 Å and an all-atom RMSD of 1.6 Å ( Figure 8A ).
(A) The best model is in blue and the actual structure in red (PDB code: 1H1W).
Publication Year: 2007
Elastic network model of allosteric regulation in protein kinase PDK1.
(2010) BMC Struct Biol 10
PubMed: 20500829 | PubMedCentral: PMC2888814 | DOI: 10.1186/1472-6807-10-11
When applied to the inactive PDK1 structure (protein data bank accession 1H1W) the same general picture emerges, see figure 6G .
Comparing this structure with the free PDK1 (1H1W) [ 5 ] it is clear that the activation loop in the C-terminal domain undergoes a conformational change upon PS48 binding to the N-terminal domain, see below.
Publication Year: 2010
Ligand-based Pharmacophore Modeling; Atom-based 3D-QSAR Analysis and Molecular Docking Studies of Phosphoinositide-Dependent Kinase-1 Inhibitors.
(2012) Indian J Pharm Sci 74
PubMed: 23325995 | PubMedCentral: PMC3546331 | DOI: 10.4103/0250-474X.103846
: In Silico Studies on PDK-1 Inhibitors REFERENCES 1 Lawlor MA Mora A Ashby PR Williams MR Murray-Tait V Malone L Essential role of PDK1 in regulating cell size and development in mice EMBO J 2002 14 ... 728 38 12110585 2 Pullen N Dennis PB Andjelkovic M Dufner A Kozma SC Hemmings BA Phosphorylation and Activation of p70s6k by PDK1 Science 1998 5351 707 10 9445476 3 Mora A Komander D van Aalten D Alessi D PDK1, the master regulator of AGC kinase signal transduction Sem Cell Dev Biol 2004 2 161 70 4 Vanhaesebroeck B Leevers SJ Ahmadi K Timms J Katso R Driscoll PC Synthesis and function of 3-Phosphorylated Inositol lipids Annu Rev Biochem 2001 1 535 602 11395417 5 Osaki M Oshimura M Ito H PI3K-Akt pathway: Its functions and alterations in human cancer Apoptosis 2004 6 667 76 15505410 6 Hanada M Feng J Hemmings BA Structure, regulation and function of PKB/AKT-a major therapeutic target Biochim Biophys Acta 2004 1-2 3 16 15023346 7 Zhang Q Thomas SM Lui VW Xi S Siegfried JM Fan H Phosphorylation of TNF- α converting enzyme by gastrin-releasing peptide induces amphiregulin release and EGF receptor activation PNAS 2006 18 6901 6 16641105 8 Baryawno N Sveinbjornsson B Eksborg S Chen CS Kogner P Johnsen JI Small-Molecule Inhibitors of Phosphatidylinositol 3-Kinase/Akt Signaling Inhibit Wnt/beta-Catenin Pathway Cross-Talk and Suppress Medulloblastoma Growth Cancer Res 2010 1 266 76 20028853 9 Zeng X Xu H Glazer RI Transformation of Mammary Epithelial Cells by 3-Phosphoinositide-dependent Protein Kinase-1 (PDK1) Is Associated with the Induction of Protein Kinase C Alpha Cancer Res 2002 12 3538 43 12068001 10 Flynn P Wong M Zavar M Dean NM Stokoe D Inhibition of PDK-1 activity causes a reduction in cell proliferation and survival Curr Biol 2000 22 1439 42 11102805 11 Berman HM Westbrook J Feng Z Gilliland G Bhat TN Weissig H The Protein Data Bank Nucleic Acids Res 2000 1 235 42 10592235 12 PDB codes: 2PE1, 1H1W, 1UVR, 1UU9, 1UU8, 1UU7, 1UU3, 1OKZ, 1OKY, 1Z5M, 3H9O, 3ION, 3IOP 13 Peifer C Alessi DR Small-Molecule Inhibitors of PDK1 Chem Med Chem 2008 12 1810 38 18972468 14 Dixon S Smondyrev A Knoll E Rao S Shaw D Friesner R PHASE: A new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1.
Publication Year: 2012
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