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Yorodumi- PDB-4c7k: 11b-Hydroxysteroid Dehydrogenase Type I in complex with inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c7k | ||||||
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Title | 11b-Hydroxysteroid Dehydrogenase Type I in complex with inhibitor | ||||||
Components | CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1 | ||||||
Keywords | OXIDOREDUCTASE / CNS PENETRATION / STRUCTURE-BASED DESIGN | ||||||
Function / homology | Function and homology information 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / 11beta-hydroxysteroid dehydrogenase / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development ...11-beta-hydroxysteroid dehydrogenase (NADP+) activity / 11beta-hydroxysteroid dehydrogenase / 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 / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Goldberg, F.W. / Dossetter, A.G. / Scott, J.S. / Robb, G.R. / Boyd, S. / Groombridge, S.D. / Kemmitt, P.D. / Sjogren, T. / Morentin Gutierrez, P. / de Schoolmeester, J. ...Goldberg, F.W. / Dossetter, A.G. / Scott, J.S. / Robb, G.R. / Boyd, S. / Groombridge, S.D. / Kemmitt, P.D. / Sjogren, T. / Morentin Gutierrez, P. / de Schoolmeester, J. / Swales, J.G. / Turnbull, A.V. / Wild, M.J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Optimization of Brain Penetrant 11Beta-Hydroxysteroid Dehydrogenase Type I Inhibitors and in Vivo Testing in Diet- Induced Obese Mice. Authors: Goldberg, F.W. / Dossetter, A.G. / Scott, J.S. / Robb, G.R. / Boyd, S. / Groombridge, S.D. / Kemmitt, P.D. / Sjogren, T. / Gutierrez, P.M. / Deschoolmeester, J. / Swales, J.G. / Turnbull, A.V. / Wild, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c7k.cif.gz | 227.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c7k.ent.gz | 183.5 KB | Display | PDB format |
PDBx/mmJSON format | 4c7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c7k_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 4c7k_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 4c7k_validation.xml.gz | 46.9 KB | Display | |
Data in CIF | 4c7k_validation.cif.gz | 67.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/4c7k ftp://data.pdbj.org/pub/pdb/validation_reports/c7/4c7k | HTTPS FTP |
-Related structure data
Related structure data | 4c7jC 4bb5S 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 29648.395 Da / Num. of mol.: 4 / Fragment: RESIDUES 24-292 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P28845, 11beta-hydroxysteroid dehydrogenase #2: Chemical | ChemComp-NAP / #3: Chemical | #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: 1.9 Å3/Da / Density % sol: 36 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 |
Detector | Type: RIGAKU HTC / Detector: IMAGE PLATE / Date: Feb 22, 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: 1.91→49.63 Å / Num. obs: 74883 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 20.14 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 1.91→1.96 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.9 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BB5 Resolution: 1.91→49.63 Å / Cor.coef. Fo:Fc: 0.9055 / Cor.coef. Fo:Fc free: 0.8536 / SU R Cruickshank DPI: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.236 / SU Rfree Blow DPI: 0.198 / SU Rfree Cruickshank DPI: 0.194 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 29.16 Å2
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Refine analyze | Luzzati coordinate error obs: 0.332 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→49.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.96 Å / Total num. of bins used: 20
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