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Yorodumi- PDB-2y5k: Orally active aminopyridines as inhibitors of tetrameric fructose... -
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-Basic information
Entry | Database: PDB / ID: 2y5k | ||||||
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Title | Orally active aminopyridines as inhibitors of tetrameric fructose 1,6- bisphosphatase | ||||||
Components | FRUCTOSE-1,6-BISPHOSPHATASE 1 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / Gluconeogenesis / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process ...cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / Gluconeogenesis / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / fructose metabolic process / monosaccharide binding / fructose 1,6-bisphosphate metabolic process / negative regulation of glycolytic process / cellular hyperosmotic salinity response / regulation of gluconeogenesis / AMP binding / dephosphorylation / cellular response to cAMP / response to nutrient levels / gluconeogenesis / negative regulation of cell growth / cellular response to insulin stimulus / cellular response to xenobiotic stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Ruf, A. / Hebeisen, P. / Haap, W. / Kuhn, B. / Mohr, P. / Wessel, H.P. / Zutter, U. / Kirchner, S. / Benz, J. / Joseph, C. ...Ruf, A. / Hebeisen, P. / Haap, W. / Kuhn, B. / Mohr, P. / Wessel, H.P. / Zutter, U. / Kirchner, S. / Benz, J. / Joseph, C. / Alvarez-Sanchez, R. / Gubler, M. / Schott, B. / Benardeau, A. / Tozzo, E. / Kitas, E. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2011 Title: Orally Active Aminopyridines as Inhibitors of Tetrameric Fructose-1,6-Bisphosphatase. Authors: Hebeisen, P. / Haap, W. / Kuhn, B. / Mohr, P. / Wessel, H.P. / Zutter, U. / Kirchner, S. / Ruf, A. / Benz, J. / Joseph, C. / Alvarez-Sanchez, R. / Gubler, M. / Schott, B. / Benardeau, A. / Tozzo, E. / Kitas, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y5k.cif.gz | 269.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y5k.ent.gz | 218.7 KB | Display | PDB format |
PDBx/mmJSON format | 2y5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/2y5k ftp://data.pdbj.org/pub/pdb/validation_reports/y5/2y5k | HTTPS FTP |
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-Related structure data
Related structure data | 2y5lC 2vt5S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 36859.418 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: LIVER / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09467, fructose-bisphosphatase #2: Chemical | ChemComp-YCU / #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: 2.61 Å3/Da / Density % sol: 52.81 % / Description: NONE |
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Crystal grow | Details: RESERVOIR: 0.1M HEPES, PH 7.0, 0.1 M AMMONIUM ACETATE, 12% PEG 3350. |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 22, 2007 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→142 Å / Num. obs: 87553 / % possible obs: 90.8 % / Observed criterion σ(I): -10 / Redundancy: 5.97 % / Biso Wilson estimate: 0.226 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.39 |
Reflection shell | Resolution: 2.06→2.19 Å / Redundancy: 3.42 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.45 / % possible all: 51.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VT5 Resolution: 2.1→29.48 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.836 / SU B: 6.615 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.749 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→29.48 Å
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Refine LS restraints |
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