+Open data
-Basic information
Entry | Database: PDB / ID: 6q8k | ||||||
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Title | CLK1 with bound pyridoquinazoline | ||||||
Components | Dual specificity protein kinase CLK1 | ||||||
Keywords | TRANSFERASE / CLK1 / Dual specifity protein kinase CLK1 / Inhibitor / Kinase / Structural Genomics / 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: 2.29 Å | ||||||
Authors | Schroeder, M. / Tazarki, H. / Zeinyeh, W. / Esvan, Y.J. / Khiari, J. / Joesselin, B. / Bach, S. / Ruchaud, S. / Anizon, F. / Giraud, F. ...Schroeder, M. / Tazarki, H. / Zeinyeh, W. / Esvan, Y.J. / Khiari, J. / Joesselin, B. / Bach, S. / Ruchaud, S. / Anizon, F. / Giraud, F. / Moreau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / 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 | 6q8k.cif.gz | 152.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q8k.ent.gz | 124.6 KB | Display | PDB format |
PDBx/mmJSON format | 6q8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/6q8k ftp://data.pdbj.org/pub/pdb/validation_reports/q8/6q8k | 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: 39581.512 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-FG9 / ~{ |
#4: 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: 2.4 Å3/Da / Density % sol: 48.76 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 255 PEG 6000. 0.1 M bicine pH 9.0 |
-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 6M-F / Detector: PIXEL / Date: Oct 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→64.25 Å / Num. obs: 16639 / % possible obs: 98 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.29→2.37 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1608 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→64.25 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.889 / SU B: 15.207 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.261 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.14 Å2
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Refinement step | Cycle: 1 / Resolution: 2.29→64.25 Å
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Refine LS restraints |
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