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- PDB-3qcq: Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 6-(... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qcq | ||||||
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Title | Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 6-(3-Amino-1H-indazol-6-yl)-N4-ethyl-2,4-pyrimidinediamine | ||||||
![]() | 3-phosphoinositide-dependent protein kinase 1 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / protein-ligand complex / Kinase / Signal transduction / ATP binding Phosphoinositide binding for full length / Phoshorylation on S241 / celluar and membrane associated / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() 3-phosphoinositide-dependent protein kinase activity / Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / positive regulation of phospholipase activity / hyperosmotic response / RSK activation / regulation of canonical NF-kappaB signal transduction / positive regulation of vascular endothelial cell proliferation ...3-phosphoinositide-dependent protein kinase activity / Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / positive regulation of phospholipase activity / hyperosmotic response / RSK activation / regulation of canonical NF-kappaB signal transduction / positive regulation of vascular endothelial cell proliferation / negative regulation of cardiac muscle cell apoptotic process / phospholipase activator activity / positive regulation of sprouting angiogenesis / Constitutive Signaling by AKT1 E17K in Cancer / CD28 dependent PI3K/Akt signaling / phospholipase binding / cellular response to epidermal growth factor stimulus / positive regulation of blood vessel endothelial cell migration / Role of LAT2/NTAL/LAB on calcium mobilization / Estrogen-stimulated signaling through PRKCZ / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of endothelial cell apoptotic process / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / extrinsic apoptotic signaling pathway / RHO GTPases activate PKNs / GPVI-mediated activation cascade / T cell costimulation / activation of protein kinase B activity / positive regulation of protein localization to plasma membrane / Integrin signaling / insulin-like growth factor receptor signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / negative regulation of transforming growth factor beta receptor signaling pathway / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / epidermal growth factor receptor signaling pathway / cell projection / peptidyl-threonine phosphorylation / calcium-mediated signaling / negative regulation of protein kinase activity / cellular response to insulin stimulus / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Regulation of TP53 Degradation / G beta:gamma signalling through PI3Kgamma / positive regulation of angiogenesis / PIP3 activates AKT signaling / cell migration / Downstream TCR signaling / insulin receptor signaling pathway / actin cytoskeleton organization / cytoplasmic vesicle / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynaptic density / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Medina, J.R. / Becker, C.J. / Blackledge, C.W. / Duquenne, C. / Feng, Y. / Grant, S.W. / Heerding, D. / Li, W.H. / Miller, W.H. / Romeril, S.P. ...Medina, J.R. / Becker, C.J. / Blackledge, C.W. / Duquenne, C. / Feng, Y. / Grant, S.W. / Heerding, D. / Li, W.H. / Miller, W.H. / Romeril, S.P. / Scherzer, D. / Shu, A. / Bobko, M.A. / Chadderton, A.R. / Dumble, M. / Gradiner, C.M. / Gilbert, S. / Liu, Q. / Rabindran, S.K. / Sudakin, V. / Xiang, H. / Brady, P.G. / Campobasso, N. / Ward, P. / Axten, J.M. | ||||||
![]() | ![]() Title: Structure-Based Design of Potent and Selective 3-Phosphoinositide-Dependent Kinase-1 (PDK1) Inhibitors. Authors: Medina, J.R. / Becker, C.J. / Blackledge, C.W. / Duquenne, C. / Feng, Y. / Grant, S.W. / Heerding, D. / Li, W.H. / Miller, W.H. / Romeril, S.P. / Scherzer, D. / Shu, A. / Bobko, M.A. / ...Authors: Medina, J.R. / Becker, C.J. / Blackledge, C.W. / Duquenne, C. / Feng, Y. / Grant, S.W. / Heerding, D. / Li, W.H. / Miller, W.H. / Romeril, S.P. / Scherzer, D. / Shu, A. / Bobko, M.A. / Chadderton, A.R. / Dumble, M. / Gardiner, C.M. / Gilbert, S. / Liu, Q. / Rabindran, S.K. / Sudakin, V. / Xiang, H. / Brady, P.G. / Campobasso, N. / Ward, P. / Axten, J.M. #1: ![]() Title: Aminoindazole PDK1 Inhibitors: A Case Study in Fragment-Based Drug Discovery Authors: Medina, J.R. / Blackledge, C.W. / Heerding, D.A. / Campobasso, N. / Ward, P. / Briand, J. / Wright, L. / Axten, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.8 KB | Display | ![]() |
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PDB format | ![]() | 54.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3qcsC ![]() 3qcxC ![]() 3qcyC ![]() 3qd0C ![]() 3qd3C ![]() 3qd4C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35652.852 Da / Num. of mol.: 1 / Fragment: kinase domain, residues 48-359 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O15530, non-specific serine/threonine protein kinase | ||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-3Q0 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.82 % |
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Crystal grow | Temperature: 323 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 1.9-2 M ammonium sulfate and 0.1 M tris pH 9 plus 15 - 30 % glycerol for freezing, VAPOR DIFFUSION, SITTING DROP, temperature 323K |
-Data collection
Diffraction | Mean temperature: 110 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. all: 14544 / Num. obs: 14515 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Rmerge(I) obs: 0.123 / Χ2: 1.007 / Net I/σ(I): 10.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.875 Å2 / ksol: 0.369 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 175.82 Å2 / Biso mean: 41.0497 Å2 / Biso min: 3.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.501→43.089 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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