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Yorodumi- PDB-5j1w: Crystal structure of human CLK1 in complex with pyrido[3,4-g]quin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j1w | ||||||
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Title | Crystal structure of human CLK1 in complex with pyrido[3,4-g]quinazoline derivative ZW31 (compound 14) | ||||||
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 / Resolution: 2.42 Å | ||||||
Authors | Chaikuad, A. / Esvan, Y.J. / Zeinyeh, W. / Boibessot, T. / Nauton, L. / Thery, V. / Loaec, N. / Meijer, L. / Giraud, F. / Moreau, P. ...Chaikuad, A. / Esvan, Y.J. / Zeinyeh, W. / Boibessot, T. / Nauton, L. / Thery, V. / Loaec, N. / Meijer, L. / Giraud, F. / Moreau, P. / Anizon, F. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2016 Title: Discovery of pyrido[3,4-g]quinazoline derivatives as CMGC family protein kinase inhibitors: Design, synthesis, inhibitory potency and X-ray co-crystal structure. Authors: Esvan, Y.J. / Zeinyeh, W. / Boibessot, T. / Nauton, L. / Thery, V. / Knapp, S. / Chaikuad, A. / Loaec, N. / Meijer, L. / 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 | 5j1w.cif.gz | 415.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j1w.ent.gz | 352.4 KB | Display | PDB format |
PDBx/mmJSON format | 5j1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/5j1w ftp://data.pdbj.org/pub/pdb/validation_reports/j1/5j1w | 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 39581.512 Da / Num. of mol.: 3 / Fragment: UNP residues 148-484 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLK1, CLK / Plasmid: pLIC-SGC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-pRARE2 / References: UniProt: P49759, dual-specificity kinase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-6FB / #4: Chemical | #5: 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: 2.51 Å3/Da / Density % sol: 51.04 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 30% 1,2-propanediol, 10% glycerol and 50 mM Na/K phosphate pH 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→35.59 Å / Num. obs: 44729 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 53.1 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.42→2.55 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Resolution: 2.42→35.59 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 19.682 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.434 / ESU R Free: 0.247 / 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: 66.211 Å2
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Refinement step | Cycle: 1 / Resolution: 2.42→35.59 Å
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Refine LS restraints |
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