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Yorodumi- PDB-1z3n: Human aldose reductase in complex with NADP+ and the inhibitor li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z3n | ||||||
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Title | Human aldose reductase in complex with NADP+ and the inhibitor lidorestat at 1.04 angstrom | ||||||
Components | aldose reductase | ||||||
Keywords | OXIDOREDUCTASE / NADP+ / LIDORESTAT | ||||||
Function / homology | Function and homology information glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase / L-ascorbic acid biosynthetic process / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / renal water homeostasis / epithelial cell maturation / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / electron transfer activity / carbohydrate metabolic process / negative regulation of apoptotic process / extracellular space / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.04 Å | ||||||
Authors | Van Zandt, M.C. / Jones, M.L. / Gunn, D.E. / Geraci, L.S. / Jones, J.H. / Sawicki, D.R. / Sredy, J. / Jacot, J.L. / Dicioccio, A.T. / Petrova, T. ...Van Zandt, M.C. / Jones, M.L. / Gunn, D.E. / Geraci, L.S. / Jones, J.H. / Sawicki, D.R. / Sredy, J. / Jacot, J.L. / Dicioccio, A.T. / Petrova, T. / Mitschler, A. / Podjarny, A.D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2005 Title: Discovery of 3-[(4,5,7-trifluorobenzothiazol-2-yl)methyl]indole-N-acetic acid (lidorestat) and congeners as highly potent and selective inhibitors of aldose reductase for treatment of chronic ...Title: Discovery of 3-[(4,5,7-trifluorobenzothiazol-2-yl)methyl]indole-N-acetic acid (lidorestat) and congeners as highly potent and selective inhibitors of aldose reductase for treatment of chronic diabetic complications Authors: Van Zandt, M.C. / Jones, M.L. / Gunn, D.E. / Geraci, L.S. / Jones, J.H. / Sawicki, D.R. / Sredy, J. / Jacot, J.L. / Dicioccio, A.T. / Petrova, T. / Mitschler, A. / Podjarny, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z3n.cif.gz | 179.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z3n.ent.gz | 142.4 KB | Display | PDB format |
PDBx/mmJSON format | 1z3n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/1z3n ftp://data.pdbj.org/pub/pdb/validation_reports/z3/1z3n | 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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Unit cell |
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-Components
#1: Protein | Mass: 36180.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 References: GenBank: 178489, UniProt: P15121*PLUS, aldose reductase |
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#2: Chemical | ChemComp-NDP / |
#3: Chemical | ChemComp-3NA / { |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Aldose Reductase, Lidorestat, NADP+, PEG 6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.95 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 22, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→15 Å / Num. all: 143784 / Num. obs: 139636 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.04 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.04→1.06 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 4.05 / Rsym value: 0.252 / % possible all: 85.4 |
-Processing
Software |
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Refinement | Resolution: 1.04→10 Å / Num. parameters: 31049 / Num. restraintsaints: 43650 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 107 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2963.86 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.04→10 Å
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Refine LS restraints |
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