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Yorodumi- PDB-4k1l: 4,4-Dioxo-5,6-dihydro-[1,4,3]oxathiazines, a novel class of 11 be... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k1l | ||||||
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Title | 4,4-Dioxo-5,6-dihydro-[1,4,3]oxathiazines, a novel class of 11 beta-HSD1 inhibitors for the treatment of diabetes | ||||||
Components | Corticosteroid 11-beta-dehydrogenase isozyme 1 | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / 11-beta-hydroxysteroid dehydrogenase 1 / 11-DH / 11-beta-HSD1 / short chain dehydrogenase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development ...11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development / NADP binding / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / protein homodimerization activity / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.96 Å | ||||||
Authors | Loenze, P. / Schimanski-Breves, S. / Von der Heyden, 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 | 4k1l.cif.gz | 233 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k1l.ent.gz | 188 KB | Display | PDB format |
PDBx/mmJSON format | 4k1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k1l_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 4k1l_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 4k1l_validation.xml.gz | 47.1 KB | Display | |
Data in CIF | 4k1l_validation.cif.gz | 66.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/4k1l ftp://data.pdbj.org/pub/pdb/validation_reports/k1/4k1l | HTTPS FTP |
-Related structure data
Related structure data | 4k26C 1xu9S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31836.875 Da / Num. of mol.: 4 / Mutation: C272S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSD11B1, HSD11, HSD11L / Production host: Escherichia coli (E. coli) References: UniProt: P28845, 11beta-hydroxysteroid dehydrogenase #2: Chemical | ChemComp-SFF / ( #3: Chemical | ChemComp-NDP / #4: 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: 2.52 Å3/Da / Density % sol: 51.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 40% PEG300, 0.1M MES, pH 6.5, vapor diffusion, temperature 277K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.96→75.46 Å / Num. all: 89991 / Num. obs: 89812 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.42 Å2 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 3.78 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 5.18 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1XU9 Resolution: 1.96→28.62 Å / Cor.coef. Fo:Fc: 0.9504 / Cor.coef. Fo:Fc free: 0.9333 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 24.77 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→28.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.01 Å / Total num. of bins used: 20
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