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Yorodumi- PDB-4k26: 4,4-Dioxo-5,6-dihydro-[1,4,3]oxathiazines, a novel class of 11 -H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k26 | ||||||
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Title | 4,4-Dioxo-5,6-dihydro-[1,4,3]oxathiazines, a novel class of 11 -HSD1 inhibitors for the treatment of diabetes | ||||||
Components | Corticosteroid 11-beta-dehydrogenase isozyme 1 | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Oxidoreductase / alpha and beta proteins / NAD(P)-binding Rossman-fold / short chain dehydrogenase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information mineralocorticoid metabolic process / Glucocorticoid biosynthesis / glucocorticoid catabolic process / regulation of pentose-phosphate shunt / glucocorticoid biosynthetic process / 11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity ...mineralocorticoid metabolic process / Glucocorticoid biosynthesis / glucocorticoid catabolic process / regulation of pentose-phosphate shunt / glucocorticoid biosynthetic process / 11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Prednisone ADME / steroid catabolic process / steroid binding / lung development / apical part of cell / NADP binding / nuclear membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.21 Å | ||||||
Authors | Loenze, P. / Schimanski-Breves, S. / Vonderheyden, C. / Engel, C.K. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2013 Title: 1,1-Dioxo-5,6-dihydro-[4,1,2]oxathiazines, a novel class of 11-HSD1 inhibitors for the treatment of diabetes. Authors: Bohme, T. / Engel, C.K. / Farjot, G. / Gussregen, S. / Haack, T. / Tschank, G. / Ritter, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k26.cif.gz | 123.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k26.ent.gz | 95.8 KB | Display | PDB format |
PDBx/mmJSON format | 4k26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k26_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 4k26_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4k26_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 4k26_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/4k26 ftp://data.pdbj.org/pub/pdb/validation_reports/k2/4k26 | HTTPS FTP |
-Related structure data
Related structure data | 4k1lC 1y5rS 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: 30585.680 Da / Num. of mol.: 2 / Fragment: murine 11-BETA-HSD_24-292 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hsd11b1, Hsd11 / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P50172, 11beta-hydroxysteroid dehydrogenase #2: Chemical | #3: Chemical | #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: 2.65 Å3/Da / Density % sol: 53.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: HEPES 100mM pH 7.5, (NH4)2SO4 1.7M, 1 mM NADP, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.21→95.82 Å / Num. obs: 32949 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.85 Å2 / Rsym value: 0.127 |
Reflection shell | Resolution: 2.21→2.28 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 4.65 / Rsym value: 0.435 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1Y5R Resolution: 2.21→19.82 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.9178 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 27.56 Å2
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Refine analyze | Luzzati coordinate error obs: 0.217 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→19.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.21→2.28 Å / Total num. of bins used: 16
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