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Yorodumi- PDB-7mgj: TNNI3K complexed with N-methyl-4-(4-(3-(3-(trifluoromethyl) pheny... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mgj | ||||||
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Title | TNNI3K complexed with N-methyl-4-(4-(3-(3-(trifluoromethyl) phenyl) ureido) phenoxy)picolinamide | ||||||
Components | Serine/threonine-protein kinase TNNI3K | ||||||
Keywords | TRANSFERASE/INHIBITOR / kinase / CARK / TRANSFERASE / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information bundle of His cell to Purkinje myocyte communication / regulation of cardiac muscle contraction / regulation of cardiac conduction / regulation of heart rate / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding ...bundle of His cell to Purkinje myocyte communication / regulation of cardiac muscle contraction / regulation of cardiac conduction / regulation of heart rate / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Shewchuk, L.M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Identification of Diarylurea Inhibitors of the Cardiac-Specific Kinase TNNI3K by Designing Selectivity Against VEGFR2, p38 alpha , and B-Raf. Authors: Patterson, J.R. / Graves, A.P. / Stoy, P. / Cheung, M. / Desai, T.A. / Fries, H. / Gatto Jr., G.J. / Holt, D.A. / Shewchuk, L. / Totoritis, R. / Wang, L. / Kallander, L.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mgj.cif.gz | 215.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mgj.ent.gz | 169.3 KB | Display | PDB format |
PDBx/mmJSON format | 7mgj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/7mgj ftp://data.pdbj.org/pub/pdb/validation_reports/mg/7mgj | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 37163.852 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNNI3K, CARK / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q59H18, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-ZFS / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.3 M NaK tartrate, 0.1M HEPES pH7 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.912→80 Å / Num. obs: 43990 / % possible obs: 98.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 62.6 Å2 / Rmerge(I) obs: 0.089 / Χ2: 1.011 / Net I/σ(I): 11.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: unpublished structure Resolution: 2.95→43.96 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.68 Å2 / Biso mean: 53.23 Å2 / Biso min: 23.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.95→43.96 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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