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Yorodumi- PDB-5eqy: Crystal structure of choline kinase alpha-1 bound by 5-[(4-methyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eqy | ||||||
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Title | Crystal structure of choline kinase alpha-1 bound by 5-[(4-methyl-1,4-diazepan-1-yl)methyl]-2-[4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]benzenecarbonitrile (compound 65) | ||||||
Components | Choline kinase alpha | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Kinase / inhibitor / drug target / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information ethanolamine kinase / choline kinase / ethanolamine kinase activity / CDP-choline pathway / choline kinase activity / Synthesis of PE / phosphatidylethanolamine biosynthetic process / lipid droplet disassembly / phosphatidylcholine biosynthetic process / cholinesterase activity ...ethanolamine kinase / choline kinase / ethanolamine kinase activity / CDP-choline pathway / choline kinase activity / Synthesis of PE / phosphatidylethanolamine biosynthetic process / lipid droplet disassembly / phosphatidylcholine biosynthetic process / cholinesterase activity / lipid transport / Synthesis of PC / cellular response to glucose starvation / lipid droplet / lipid metabolic process / protein tyrosine kinase activity / phosphorylation / protein homodimerization activity / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Zhou, T. / Zhu, X. / Dalgarno, D.C. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Novel Small Molecule Inhibitors of Choline Kinase Identified by Fragment-Based Drug Discovery. Authors: Zech, S.G. / Kohlmann, A. / Zhou, T. / Li, F. / Squillace, R.M. / Parillon, L.E. / Greenfield, M.T. / Miller, D.P. / Qi, J. / Thomas, R.M. / Wang, Y. / Xu, Y. / Miret, J.J. / Shakespeare, W. ...Authors: Zech, S.G. / Kohlmann, A. / Zhou, T. / Li, F. / Squillace, R.M. / Parillon, L.E. / Greenfield, M.T. / Miller, D.P. / Qi, J. / Thomas, R.M. / Wang, Y. / Xu, Y. / Miret, J.J. / Shakespeare, W.C. / Zhu, X. / Dalgarno, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eqy.cif.gz | 160.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eqy.ent.gz | 124.2 KB | Display | PDB format |
PDBx/mmJSON format | 5eqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/5eqy ftp://data.pdbj.org/pub/pdb/validation_reports/eq/5eqy | HTTPS FTP |
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-Related structure data
Related structure data | 5eqeC 5eqpC 3g15S C: citing same article (ref.) S: Starting model for refinement |
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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: 46856.477 Da / Num. of mol.: 2 / Fragment: UNP residues 75-457 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHKA, CHK, CKI / Production host: Escherichia coli (E. coli) References: UniProt: P35790, choline kinase, ethanolamine kinase #2: Chemical | #3: 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: 2.35 Å3/Da / Density % sol: 47.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M sodium formate, 8-12% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 28, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 31277 / % possible obs: 99.5 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.079 / Χ2: 1.038 / Net I/av σ(I): 22.929 / Net I/σ(I): 9.3 / Num. measured all: 185192 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3G15 Resolution: 2.5→50 Å / FOM work R set: 0.787 / Cross valid method: FREE R-VALUE / σ(F): 0
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Displacement parameters | Biso max: 116.1 Å2 / Biso mean: 49.9295 Å2 / Biso min: 18.75 Å2
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Refinement step | Cycle: final / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29
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Xplor file |
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