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Yorodumi- PDB-3g9n: JNK3 bound to (Z)-1-((6-fluoro-4H-benzo[d][1,3]dioxin-8-yl)methyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g9n | ||||||
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Title | JNK3 bound to (Z)-1-((6-fluoro-4H-benzo[d][1,3]dioxin-8-yl)methyl)-3-(hydroxyimino)-4-phenylindolin-2-one | ||||||
Components | Mitogen-activated protein kinase 10 | ||||||
Keywords | TRANSFERASE / kinase / inhibitor / phosphorylation / ATP-binding / Epilepsy / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase | ||||||
Function / homology | Function and homology information JUN kinase activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / response to light stimulus / mitogen-activated protein kinase / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation / regulation of circadian rhythm ...JUN kinase activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / response to light stimulus / mitogen-activated protein kinase / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation / regulation of circadian rhythm / cellular senescence / rhythmic process / Oxidative Stress Induced Senescence / protein phosphorylation / protein serine kinase activity / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Jacobs, M.D. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: Structure-based design and parallel synthesis of N-benzyl isatin oximes as JNK3 MAP kinase inhibitors. Authors: Cao, J. / Gao, H. / Bemis, G. / Salituro, F. / Ledeboer, M. / Harrington, E. / Wilke, S. / Taslimi, P. / Pazhanisamy, S. / Xie, X. / Jacobs, M. / Green, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g9n.cif.gz | 82.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g9n.ent.gz | 62.2 KB | Display | PDB format |
PDBx/mmJSON format | 3g9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/3g9n ftp://data.pdbj.org/pub/pdb/validation_reports/g9/3g9n | 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: 42116.727 Da / Num. of mol.: 1 / Fragment: kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JNK3, JNK3A, MAPK10, PRKM10 / Plasmid: pET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P53779, mitogen-activated protein kinase |
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#2: Chemical | ChemComp-J88 / ( |
#3: 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: 2.32 Å3/Da / Density % sol: 46.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18-20% (v/v) polyethylene glycol monomethyl ether (average Mr = 550), 10% (v/v) ethylene glycol, 20 mM beta-mercaptoethanol, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 2, 1999 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→59.87 Å / Num. obs: 9652 / % possible obs: 82.4 % / Rmerge(I) obs: 0.098 / Χ2: 1.165 / Net I/σ(I): 8.501 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 2.8→55 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.809 / WRfactor Rfree: 0.308 / WRfactor Rwork: 0.224 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.773 / SU B: 21.372 / SU ML: 0.418 / SU R Cruickshank DPI: 0.406 / SU Rfree: 0.542 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.525 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.8 Å2 / Biso mean: 37.763 Å2 / Biso min: 8.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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Refinement TLS params. | L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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