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Yorodumi- PDB-4ise: Human glucokinase in complex with novel activator (2S)-3-cyclohex... -
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-Basic information
Entry | Database: PDB / ID: 4ise | ||||||
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Title | Human glucokinase in complex with novel activator (2S)-3-cyclohexyl-2-(6-fluoro-4-oxoquinazolin-3(4H)-yl)-N-(1,3-thiazol-2-yl)propanamide | ||||||
Components | Glucokinase | ||||||
Keywords | TRANSFERASE/TRANSFERASE ACTIVATOR / transferase/activator activity / glucose conversion to G6P / phosphorylation / TRANSFERASE-TRANSFERASE ACTIVATOR complex | ||||||
Function / homology | Function and homology information Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / mannokinase activity / glucose sensor activity / regulation of potassium ion transport / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose catabolic process / glucose 6-phosphate metabolic process ...Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / mannokinase activity / glucose sensor activity / regulation of potassium ion transport / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose catabolic process / glucose 6-phosphate metabolic process / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / NADP metabolic process / glucose binding / calcium ion import / cellular response to leptin stimulus / canonical glycolysis / Glycolysis / regulation of glycolytic process / intracellular glucose homeostasis / Regulation of gene expression in beta cells / regulation of insulin secretion / positive regulation of glycogen biosynthetic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / response to glucose / glycolytic process / positive regulation of insulin secretion / cellular response to insulin stimulus / glucose metabolic process / glucose homeostasis / mitochondrion / nucleoplasm / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.78 Å | ||||||
Authors | Hosfield, D. / Skene, R.J. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2013 Title: Design, synthesis and SAR of novel glucokinase activators. Authors: Cheruvallath, Z.S. / Gwaltney, S.L. / Sabat, M. / Tang, M. / Feng, J. / Wang, H. / Miura, J. / Guntupalli, P. / Jennings, A. / Hosfield, D. / Lee, B. / Wu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ise.cif.gz | 191 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ise.ent.gz | 151.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ise.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/4ise ftp://data.pdbj.org/pub/pdb/validation_reports/is/4ise | 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: 51392.527 Da / Num. of mol.: 1 / Fragment: UNP residues 16-465 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GCK, HXK4 Isoform II / Plasmid: pFLAG-CTC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5[alpha] / References: UniProt: P35557, glucokinase |
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#2: Sugar | ChemComp-GLC / |
#3: Chemical | ChemComp-1FW / ( |
#4: Chemical | ChemComp-IOD / |
#5: 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: 2.23 Å3/Da / Density % sol: 44.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 15% PEG3350, 200 mM ammonium iodide, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2006 |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. all: 44990 / Num. obs: 41700 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.78→1.84 Å / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.78→45.64 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.725 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.276 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→45.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.825 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 4.5697 Å / Origin y: 46.4695 Å / Origin z: 38.9077 Å
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Refinement TLS group |
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