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Yorodumi- PDB-2xck: Crystal structure of PDK1 in complex with a pyrazoloquinazoline i... -
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-Basic information
Entry | Database: PDB / ID: 2xck | ||||||
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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 / ATP-BINDING / SERINE/THREONINE-PROTEIN KINASE | ||||||
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 / 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 | 2xck.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xck.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 2xck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xck_validation.pdf.gz | 731.7 KB | Display | wwPDB validaton report |
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Full document | 2xck_full_validation.pdf.gz | 739.3 KB | Display | |
Data in XML | 2xck_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 2xck_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/2xck ftp://data.pdbj.org/pub/pdb/validation_reports/xc/2xck | HTTPS FTP |
-Related structure data
Related structure data | 2xchC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 35429.582 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-MH4 / | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | #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 PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 18571 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.51 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H1W Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.743 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.21 / 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: 28.563 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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