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Yorodumi- PDB-2xch: Crystal structure of PDK1 in complex with a pyrazoloquinazoline i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xch | ||||||
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Title | Crystal structure of PDK1 in complex with a pyrazoloquinazoline inhibitor | ||||||
Components | 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1 | ||||||
Keywords | TRANSFERASE / PI3-KINASE SIGNALLING / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING | ||||||
Function / homology | Function and homology information 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 / RSK activation / hyperosmotic response / regulation of canonical NF-kappaB signal transduction / negative regulation of cardiac muscle cell apoptotic process ...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 / RSK activation / hyperosmotic response / regulation of canonical NF-kappaB signal transduction / negative regulation of cardiac muscle cell apoptotic process / positive regulation of vascular endothelial cell proliferation / phospholipase activator activity / positive regulation of sprouting angiogenesis / Constitutive Signaling by AKT1 E17K in Cancer / phospholipase binding / CD28 dependent PI3K/Akt signaling / 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 / cellular response to epidermal growth factor stimulus / GPVI-mediated activation cascade / T cell costimulation / activation of protein kinase B activity / Integrin signaling / positive regulation of release of sequestered calcium ion into cytosol / insulin-like growth factor receptor signaling pathway / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / cell projection / calcium-mediated signaling / positive regulation of protein localization to plasma membrane / negative regulation of transforming growth factor beta receptor signaling pathway / peptidyl-threonine phosphorylation / negative regulation of protein kinase activity / epidermal growth factor receptor signaling pathway / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / G beta:gamma signalling through PI3Kgamma / cellular response to insulin stimulus / positive regulation of angiogenesis / cell migration / Regulation of TP53 Degradation / Downstream TCR signaling / PIP3 activates AKT signaling / insulin receptor signaling pathway / cytoplasmic vesicle / actin cytoskeleton organization / postsynaptic density / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Angiolini, M. / Banfi, P. / Casale, E. / Casuscelli, F. / Fiorelli, C. / Saccardo, M.B. / Silvagni, M. / Zuccotto, F. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: Structure-Based Optimization of Potent Pdk1 Inhibitors. Authors: Angiolini, M. / Banfi, P. / Casale, E. / Casuscelli, F. / Fiorelli, C. / Saccardo, M.B. / Silvagni, M. / Zuccotto, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xch.cif.gz | 78.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xch.ent.gz | 57.7 KB | Display | PDB format |
PDBx/mmJSON format | 2xch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/2xch ftp://data.pdbj.org/pub/pdb/validation_reports/xc/2xch | HTTPS FTP |
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-Related structure data
Related structure data | 2xckC 1h1wS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35427.609 Da / Num. of mol.: 1 / Fragment: KINASE CATALYTIC DOMAIN, RESIDUES 1-309 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: O15530, non-specific serine/threonine protein kinase | ||||
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#2: Chemical | ChemComp-CKG / | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.3 % / Description: NONE |
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Crystal grow | Details: 2.0 M AMMONIUM SULFATE,0.1 M TRIS PH8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 27, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 27886 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 4 % / Rmerge(I) obs: 0.39 / % possible all: 99.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H1W Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.104 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.771 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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