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- PDB-3pwy: Crystal structure of an extender (SPD28345)-modified human PDK1 c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pwy | ||||||
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Title | Crystal structure of an extender (SPD28345)-modified human PDK1 complex 2 | ||||||
![]() | 3-phosphoinositide-dependent protein kinase 1 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / kinase / fragment-based drug discovery / tethering with extenders / 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 / 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 / insulin-like growth factor receptor signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / cell projection / positive regulation of protein localization to plasma membrane / peptidyl-threonine phosphorylation / calcium-mediated signaling / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of protein kinase activity / epidermal growth factor receptor signaling pathway / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / cellular response to insulin stimulus / G beta:gamma signalling through PI3Kgamma / positive regulation of angiogenesis / Regulation of TP53 Degradation / cell migration / Downstream TCR signaling / insulin receptor signaling pathway / PIP3 activates AKT signaling / actin cytoskeleton organization / cytoplasmic vesicle / protein autophosphorylation / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Elling, R.A. / Penny, D.M. / Simmons, R.L. / Erlanson, D.A. / Romanowski, M.J. | ||||||
![]() | ![]() Title: Discovery of a potent and highly selective PDK1 inhibitor via fragment-based drug discovery. Authors: Erlanson, D.A. / Arndt, J.W. / Cancilla, M.T. / Cao, K. / Elling, R.A. / English, N. / Friedman, J. / Hansen, S.K. / Hession, C. / Joseph, I. / Kumaravel, G. / Lee, W.C. / Lind, K.E. / ...Authors: Erlanson, D.A. / Arndt, J.W. / Cancilla, M.T. / Cao, K. / Elling, R.A. / English, N. / Friedman, J. / Hansen, S.K. / Hession, C. / Joseph, I. / Kumaravel, G. / Lee, W.C. / Lind, K.E. / McDowell, R.S. / Miatkowski, K. / Nguyen, C. / Nguyen, T.B. / Park, S. / Pathan, N. / Penny, D.M. / Romanowski, M.J. / Scott, D. / Silvian, L. / Simmons, R.L. / Tangonan, B.T. / Yang, W. / Sun, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.9 KB | Display | ![]() |
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PDB format | ![]() | 51.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3qc4C ![]() 1h1wS S: Starting model for refinement 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: 35459.762 Da / Num. of mol.: 1 / Fragment: kinase domain (UNP residues 51-359) / Mutation: E166C, C260S 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-SYP / |
Nonpolymer details | LIGAND SYP WAS N-{2-[6-(2-MERCAPTO-ETHYLAMINO)-PYRIMIDIN-4-YLAMINO]-ETHYL}-ACRYLAMIDE PRIOR TO ...LIGAND SYP WAS N-{2-[6-(2-MERCAPTO-ETHYLAMINO |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.1 M Tris pH 7.4, 2.1 M ammonium sulfate; 16 mg/ml protein in 50 mM Tris pH 8, 400 mM KCl, 3 mM DTT; supplemented with 20 mM DTT prior to addition of inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 12, 2006 Details: 1-m-long Rh-coated bent cylindrical mirror for horizontal and vertical focusing |
Radiation | Monochromator: Double-crystal, parallel monochromator; crystal type Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→100 Å / Num. all: 14428 / Num. obs: 5005 / % possible obs: 93.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rsym value: 0.135 / Net I/σ(I): 5.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1H1W Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.822 / SU B: 34.64 / SU ML: 0.556 / Cross valid method: THROUGHOUT / ESU R Free: 0.73 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 32.27 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.619 Å / Total num. of bins used: 15
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