+Open data
-Basic information
Entry | Database: PDB / ID: 2uzt | ||||||
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Title | PKA structures of AKT, indazole-pyridine inhibitors | ||||||
Components |
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Keywords | TRANSFERASE / CAMP / KINASE / MYRISTATE / LIPOPROTEIN / SERINE/THREONINE-PROTEIN KINASE / PHOSPHORYLATION / PROTEIN KINASE A / NUCLEOTIDE-BINDING / PROTEIN KINASE INHIBITOR / ATP- BINDING / AKT INHIBITORS / NUCLEAR PROTEIN | ||||||
Function / homology | Function and homology information CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production ...CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / Recruitment of NuMA to mitotic centrosomes / VEGFA-VEGFR2 Pathway / PKA activation / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / Mitochondrial protein degradation / cAMP-dependent protein kinase complex / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / AMP-activated protein kinase activity / Vasopressin regulates renal water homeostasis via Aquaporins / protein kinase A regulatory subunit binding / mesoderm formation / sperm flagellum / negative regulation of TORC1 signaling / protein kinase A signaling / acrosomal vesicle / neuromuscular junction / cellular response to heat / peptidyl-serine phosphorylation / protein kinase activity / protein domain specific binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å | ||||||
Authors | Zhu, G.D. / Gandhi, V.B. / Gong, J. / Thomas, S. / Woods, K.W. / Song, X. / Li, T. / Diebold, R.B. / Luo, Y. / Liu, X. ...Zhu, G.D. / Gandhi, V.B. / Gong, J. / Thomas, S. / Woods, K.W. / Song, X. / Li, T. / Diebold, R.B. / Luo, Y. / Liu, X. / Guan, R. / Klinghofer, V. / Johnson, E.F. / Bouska, J. / Olson, A. / Marsh, K.C. / Stoll, V.S. / Mamo, M. / Polakowski, J. / Campbell, T.J. / Penning, T.D. / Li, Q. / Rosenberg, S.H. / Giranda, V.L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2007 Title: Syntheses of Potent, Selective, and Orally Bioavailable Indazole-Pyridine Series of Protein Kinase B/Akt Inhibitors with Reduced Hypotension. Authors: Zhu, G.D. / Gandhi, V.B. / Gong, J. / Thomas, S. / Woods, K.W. / Song, X. / Li, T. / Diebold, R.B. / Luo, Y. / Liu, X. / Guan, R. / Klinghofer, V. / Johnson, E.F. / Bouska, J. / Olson, A. / ...Authors: Zhu, G.D. / Gandhi, V.B. / Gong, J. / Thomas, S. / Woods, K.W. / Song, X. / Li, T. / Diebold, R.B. / Luo, Y. / Liu, X. / Guan, R. / Klinghofer, V. / Johnson, E.F. / Bouska, J. / Olson, A. / Marsh, K.C. / Stoll, V.S. / Mamo, M. / Polakowski, J. / Campbell, T.J. / Martin, R.L. / Gintant, G.A. / Penning, T.D. / Li, Q. / Rosenberg, S.H. / Giranda, V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uzt.cif.gz | 85.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uzt.ent.gz | 64.5 KB | Display | PDB format |
PDBx/mmJSON format | 2uzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/2uzt ftp://data.pdbj.org/pub/pdb/validation_reports/uz/2uzt | HTTPS FTP |
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-Related 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: 39216.059 Da / Num. of mol.: 1 / Fragment: RESIDUES 15-350 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00517, cAMP-dependent protein kinase |
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#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-24 / Source method: obtained synthetically / Source: (synth.) BOS TAURUS (cattle) / References: UniProt: Q3SX13 |
#3: Chemical | ChemComp-SS3 / ( |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.33 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 28058 / % possible obs: 88 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.1→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.2031 Å2 / ksol: 0.395888 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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