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Yorodumi- PDB-3zo4: The Synthesis and Evaluation of Diazaspirocyclic Protein Kinase I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zo4 | ||||||
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Title | The Synthesis and Evaluation of Diazaspirocyclic Protein Kinase Inhibitors | ||||||
Components | (CAMP-DEPENDENT PROTEIN KINASE ...Protein kinase A) x 2 | ||||||
Keywords | TRANSFERASE/INHIBITOR / TRANSFERASE-INHIBITOR COMPLEX | ||||||
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 / 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 / protein kinase A signaling / negative regulation of TORC1 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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Allen, C.E. / Chow, C.L. / Caldwell, J.J. / Westwood, I.M. / van Montfort, R.L. / Collins, I. | ||||||
Citation | Journal: Bioorg. Med. Chem. / Year: 2013 Title: Synthesis and evaluation of heteroaryl substituted diazaspirocycles as scaffolds to probe the ATP-binding site of protein kinases. Authors: Allen, C.E. / Chow, C.L. / Caldwell, J.J. / Westwood, I.M. / van Montfort, R.L. / Collins, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zo4.cif.gz | 171.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zo4.ent.gz | 133.2 KB | Display | PDB format |
PDBx/mmJSON format | 3zo4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/3zo4 ftp://data.pdbj.org/pub/pdb/validation_reports/zo/3zo4 | HTTPS FTP |
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-Related structure data
Related structure data | 3zo1C 3zo2C 3zo3C 2gfcS 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
-CAMP-DEPENDENT PROTEIN KINASE ... , 2 types, 2 molecules AI
#1: Protein | Mass: 40837.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00517, cAMP-dependent protein kinase |
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#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: RESIDUES 6-25 / Source method: obtained synthetically / Source: (synth.) BOS TAURUS (cattle) / References: UniProt: Q3SX13 |
-Non-polymers , 5 types, 451 molecules
#3: Chemical | ChemComp-MPD / ( |
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#4: Chemical | ChemComp-QWI / |
#5: Chemical | ChemComp-GOL / |
#6: Chemical | ChemComp-DMS / |
#7: 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: 2.73 Å3/Da / Density % sol: 54.9 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 6.5 Details: 25MM MES-BISTRIS PH6.5, 75MM LICL, 1MM DTT, 0.1MM EDTA, 1.5MM MEGA8; 4 DEGREES CELSIUS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→55.12 Å / Num. obs: 54405 / % possible obs: 99.7 % / Observed criterion σ(I): 1.5 / Redundancy: 4.4 % / Biso Wilson estimate: 26.35 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GFC Resolution: 1.65→55.12 Å / Cor.coef. Fo:Fc: 0.9621 / Cor.coef. Fo:Fc free: 0.9576 / SU R Cruickshank DPI: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.086 / SU Rfree Blow DPI: 0.084 / SU Rfree Cruickshank DPI: 0.081 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
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Displacement parameters | Biso mean: 29.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→55.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.69 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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