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- PDB-2pe2: CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KIN... -
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Basic information
Entry | Database: PDB / ID: 2pe2 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1) 3-{5-[2-Oxo-5-ureido-1,2-dihydro-indol-(3Z)-ylidenemethyl]-1H-pyrrol-3-yl}-N-(2-piperidin-1-yl-ethyl)-benzamide COMPLEX | ||||||
![]() | 3-phosphoinositide-dependent protein kinase 1 | ||||||
![]() | TRANSFERASE / PROTEIN INHIBITOR COMPLEX / SERINE KINASE | ||||||
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 / RSK activation / hyperosmotic response / 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 / RSK activation / hyperosmotic response / 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 / calcium-mediated signaling / positive regulation of protein localization to plasma membrane / peptidyl-threonine phosphorylation / 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 / G beta:gamma signalling through PI3Kgamma / cellular response to insulin stimulus / positive regulation of angiogenesis / Regulation of TP53 Degradation / cell migration / Downstream TCR signaling / insulin receptor signaling pathway / PIP3 activates AKT signaling / cytoplasmic vesicle / actin cytoskeleton organization / 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 / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Whitlow, M. / Adler, M. | ||||||
![]() | ![]() Title: Indolinone based phosphoinositide-dependent kinase-1 (PDK1) inhibitors. Part 2: Optimization of BX-517. Authors: Islam, I. / Brown, G. / Bryant, J. / Hrvatin, P. / Kochanny, M.J. / Phillips, G.B. / Yuan, S. / Adler, M. / Whitlow, M. / Lentz, D. / Polokoff, M.A. / Wu, J. / Shen, J. / Walters, J. / Ho, E. ...Authors: Islam, I. / Brown, G. / Bryant, J. / Hrvatin, P. / Kochanny, M.J. / Phillips, G.B. / Yuan, S. / Adler, M. / Whitlow, M. / Lentz, D. / Polokoff, M.A. / Wu, J. / Shen, J. / Walters, J. / Ho, E. / Subramanyam, B. / Zhu, D. / Feldman, R.I. / Arnaiz, D.O. #1: ![]() Title: Indolinone based Phhosphoinositide-Dependent Kinase-1 (PDK1) inhibitors- Part 1: Design, Synthesis and Billogical Activity Authors: Islam, I. / Bryant, J. / Chou, Y.-L. / Kochanny, M.J. / Lee, W. / Phillips, G.B. / Yu, H. / Adler, M. / Whitlow, M. / Ho, E. / Lentz, D. / Polokoff, M.A. / Subramanyam, B. / Wu, J.M. / Zhu, ...Authors: Islam, I. / Bryant, J. / Chou, Y.-L. / Kochanny, M.J. / Lee, W. / Phillips, G.B. / Yu, H. / Adler, M. / Whitlow, M. / Ho, E. / Lentz, D. / Polokoff, M.A. / Subramanyam, B. / Wu, J.M. / Zhu, D. / Feldman, R.I. / Arnaiz, D.O. #2: ![]() Title: Novel Small Molecule Inhibitors of 3-Phosphoinositide-Dependent Kinase-1. Authors: Feldman, R.I. / Wu, J.M. / Polokoff, M.A. / Kochanny, M.J. / Dinter, H. / Zhu, D. / Biroc, S.L. / Alicke, B. / Bryant, J. / Yuan, S. / Buckman, B.O. / Lentz, D. / Ferrer, M. / Whitlow, M. / ...Authors: Feldman, R.I. / Wu, J.M. / Polokoff, M.A. / Kochanny, M.J. / Dinter, H. / Zhu, D. / Biroc, S.L. / Alicke, B. / Bryant, J. / Yuan, S. / Buckman, B.O. / Lentz, D. / Ferrer, M. / Whitlow, M. / Adler, M. / Finster, S. / Chang, Z. / Arnaiz, D.O. #3: ![]() Title: High Resolution Crystal Structure of the Human Pdk1 Catalytic Domain Defines the Regulatory Phosphopeptide Docking Site. Authors: Biondi, R.M. / Komander, D. / Thomas, C.C. / Lizcano, J.M. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.4 KB | Display | ![]() |
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PDB format | ![]() | 58.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 713.3 KB | Display | ![]() |
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Full document | ![]() | 716.2 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 33130.117 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN 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 | #3: Chemical | ChemComp-464 / | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: AMMONIUM SULFATE, TRIS, EDTA, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 30, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→50 Å / Num. obs: 22919 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.28 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.0665 / Net I/σ(I): 9.95 |
Reflection shell | Resolution: 2.13→2.26 Å / Redundancy: 3.16 % / Mean I/σ(I) obs: 1.72 / Rsym value: 0.3512 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER PLUS REFINEMENT Resolution: 2.13→19.72 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 137258.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 71.76 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.13→19.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.13→2.26 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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