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Yorodumi- PDB-6q8p: Structure of CLK1 with bound N-methyl-10-nitropyrido[3,4-g]quinaz... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q8p | ||||||
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Title | Structure of CLK1 with bound N-methyl-10-nitropyrido[3,4-g]quinazolin-2-amine | ||||||
Components | Dual specificity protein kinase CLK1 | ||||||
Keywords | TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / TYROSINE-PROTEIN KINASE / NUCLEUS / INHIBITOR / STRUCTURAL GENOMICS CONSORTIUM / SGC | ||||||
Function / homology | Function and homology information dual-specificity kinase / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / non-membrane spanning protein tyrosine kinase activity / protein tyrosine kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Joerger, A.C. / Chatterjee, D. / Schroeder, M. / Tazarki, H. / Zeinyeh, W. / Esvan, Y.J. / Khiari, J. / Josselin, B. / Baratte, B. / Bach, S. ...Joerger, A.C. / Chatterjee, D. / Schroeder, M. / Tazarki, H. / Zeinyeh, W. / Esvan, Y.J. / Khiari, J. / Josselin, B. / Baratte, B. / Bach, S. / Ruchaud, S. / Anizon, F. / Giraud, F. / Moreau, P. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Eur J Med Chem / Year: 2019 Title: New pyrido[3,4-g]quinazoline derivatives as CLK1 and DYRK1A inhibitors: synthesis, biological evaluation and binding mode analysis. Authors: Tazarki, H. / Zeinyeh, W. / Esvan, Y.J. / Knapp, S. / Chatterjee, D. / Schroder, M. / Joerger, A.C. / Khiari, J. / Josselin, B. / Baratte, B. / Bach, S. / Ruchaud, S. / Anizon, F. / Giraud, F. / Moreau, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q8p.cif.gz | 208.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q8p.ent.gz | 165.1 KB | Display | PDB format |
PDBx/mmJSON format | 6q8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q8p_validation.pdf.gz | 459.7 KB | Display | wwPDB validaton report |
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Full document | 6q8p_full_validation.pdf.gz | 462 KB | Display | |
Data in XML | 6q8p_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 6q8p_validation.cif.gz | 45.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/6q8p ftp://data.pdbj.org/pub/pdb/validation_reports/q8/6q8p | HTTPS FTP |
-Related structure data
Related structure data | 6q8kC 5v1jS 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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Unit cell |
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-Components
#1: Protein | Mass: 39581.512 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLK1, CLK / Production host: Escherichia coli (E. coli) / References: UniProt: P49759, dual-specificity kinase #2: Chemical | #3: Chemical | ChemComp-K / | #4: Water | ChemComp-HOH / | |
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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: 2.55 Å3/Da / Density % sol: 51.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein solution: 7-8 mg/ml protein in 30 mM Hepes, pH 7.5, 300 mM NaCl, 50 mM arginine/glutamine mix 1:1, 0.5 mM TCEP, and 1% v/v glycerol. Reservoir solution: 29% (v/v) 1,2 propanediol, 0. ...Details: Protein solution: 7-8 mg/ml protein in 30 mM Hepes, pH 7.5, 300 mM NaCl, 50 mM arginine/glutamine mix 1:1, 0.5 mM TCEP, and 1% v/v glycerol. Reservoir solution: 29% (v/v) 1,2 propanediol, 0.08 M Na/K phosphate. Crystals were soaked for 72 h in reservoir solution complemented with 1 mM compound and 20% ethylene glycol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 3→47.1 Å / Num. obs: 23961 / % possible obs: 100 % / Redundancy: 3.5 % / CC1/2: 0.973 / Rmerge(I) obs: 0.162 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.683 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5v1j Resolution: 3→45.39 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.59 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→45.39 Å
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Refine LS restraints |
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LS refinement shell |
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