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Yorodumi- PDB-3pdj: Crystal Structure of Human 11-beta-Hydroxysteroid Dehydrogenase 1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pdj | ||||||
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Title | Crystal Structure of Human 11-beta-Hydroxysteroid Dehydrogenase 1 (11b-HSD1) in Complex with 4,4-Disubstituted Cyclohexylbenzamide Inhibitor | ||||||
Components | Corticosteroid 11-beta-dehydrogenase isozyme 1 | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / 11beta / hydroxysteroid / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Wang, Z. / Sudom, A. / Walker, N.P. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2011 Title: Synthesis and Optimization of Novel 4,4-Disubstituted Cyclohexylbenzamide Derivatives as Potent 11beta-HSD1 Inhibitors Authors: Sun, D. / Wang, Z. / Caille, S. / DeGraffenreid, M. / Gonzalez-Lopez de Turiso, F. / Hungate, R. / Jaen, J.C. / Jiang, B. / Julian, L.D. / Kelly, R. / McMinn, D.L. / Kaizerman, J. / Rew, Y. ...Authors: Sun, D. / Wang, Z. / Caille, S. / DeGraffenreid, M. / Gonzalez-Lopez de Turiso, F. / Hungate, R. / Jaen, J.C. / Jiang, B. / Julian, L.D. / Kelly, R. / McMinn, D.L. / Kaizerman, J. / Rew, Y. / Sudom, A. / Tu, H. / Ursu, S. / Walker, N. / Willcockson, M. / Yan, X. / Ye, Q. / Powers, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pdj.cif.gz | 125 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pdj.ent.gz | 97.7 KB | Display | PDB format |
PDBx/mmJSON format | 3pdj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/3pdj ftp://data.pdbj.org/pub/pdb/validation_reports/pd/3pdj | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Unit cell |
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-Components
#1: Protein | Mass: 30106.982 Da / Num. of mol.: 2 / Fragment: 11b-HSD1, UNP residues 24-292 / Mutation: C272S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSD11, HSD11B1, HSD11L / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): DH10a References: UniProt: P28845, 11beta-hydroxysteroid dehydrogenase #2: Chemical | #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: 3.65 Å3/Da / Density % sol: 66.31 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 6.4 Details: 19% PEG 3350, 0.1 M MES 6.4, vapor diffusion, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSCQ315 / Detector: CCD / Date: Jan 24, 2006 / Details: 3X3 CCD ARRAY | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE-CRYSTAL, SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→92.848 Å / Num. all: 39694 / Num. obs: 39634 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 10.5 % / Biso Wilson estimate: 53.7 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 23.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→92.848 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2531 / WRfactor Rwork: 0.2226 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8083 / SU B: 5.962 / SU ML: 0.145 / SU R Cruickshank DPI: 0.2401 / SU Rfree: 0.1971 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.07 Å2 / Biso mean: 48.2051 Å2 / Biso min: 21.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→92.848 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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