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Yorodumi- PDB-7ksi: Thiophenyl-Pyrazolourea Derivatives as Potent, Brian Penetrant, O... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ksi | ||||||
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Title | Thiophenyl-Pyrazolourea Derivatives as Potent, Brian Penetrant, Orally Bioavailable, and Isoform-Selective JNK3 Inhibitors | ||||||
Components | Mitogen-activated protein kinase 10 | ||||||
Keywords | TRANSFERASE/Inhibitor / JNK3 / Kinase Inhibitor / Alzheimer Disease / Pyrazolourea / Neurodegeneration / TRANSFERASE / TRANSFERASE-Inhibitor complex | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.726 Å | ||||||
Authors | Park, H. | ||||||
Funding support | 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2021 Title: Thiophene-Pyrazolourea Derivatives as Potent, Orally Bioavailable, and Isoform-Selective JNK3 Inhibitors. Authors: Feng, Y. / Park, H. / Bauer, L. / Ryu, J.C. / Yoon, S.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ksi.cif.gz | 225.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ksi.ent.gz | 181.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ksi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/7ksi ftp://data.pdbj.org/pub/pdb/validation_reports/ks/7ksi | HTTPS FTP |
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-Related structure data
Related structure data | 7ksjC 7kskC 1jnkS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 52649.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK10, JNK3, JNK3A, PRKM10, SAPK1B / Production host: Escherichia coli (E. coli) References: UniProt: P53779, mitogen-activated protein kinase |
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#2: Chemical | ChemComp-X3S / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.92 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium tartrate pH 7.0, 20 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Sep 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.726→53.7 Å / Num. obs: 26687 / % possible obs: 86.9 % / Redundancy: 4.5 % / CC1/2: 0.999 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.726→1.808 Å / Num. unique obs: 1335 / CC1/2: 0.613 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JNK Resolution: 1.726→53.7 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.864 / SU R Cruickshank DPI: 0.477 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.228 / SU Rfree Blow DPI: 0.183 / SU Rfree Cruickshank DPI: 0.177
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Displacement parameters | Biso max: 106.42 Å2 / Biso mean: 33.77 Å2 / Biso min: 8.85 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.726→53.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.73→1.76 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
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Refinement TLS params. | Method: refined / Origin x: 16.4394 Å / Origin y: 15.2457 Å / Origin z: 23.8835 Å
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Refinement TLS group | Selection details: { A|* } |