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Yorodumi- PDB-4qx4: Human Aldose Reductase complexed with a ligand with a new scaffol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qx4 | ||||||
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Title | Human Aldose Reductase complexed with a ligand with a new scaffold at 1.26 A | ||||||
Components | Aldose reductase | ||||||
Keywords | oxidoreductase/oxidoreductase inhibitor / TIM BARREL / OXIDOREDUCTASE / oxidoreductase-oxidoreductase inhibitor complex | ||||||
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 / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / L-ascorbic acid biosynthetic process / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / renal water homeostasis / daunorubicin metabolic process / doxorubicin metabolic process / epithelial cell maturation / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / carbohydrate metabolic process / electron transfer activity / negative regulation of apoptotic process / extracellular space / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.259 Å | ||||||
Authors | Rechlin, C. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Identification of novel aldose reductase inhibitors based on carboxymethylated mercaptotriazinoindole scaffold. Authors: Stefek, M. / Soltesova Prnova, M. / Majekova, M. / Rechlin, C. / Heine, A. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qx4.cif.gz | 158 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qx4.ent.gz | 123.4 KB | Display | PDB format |
PDBx/mmJSON format | 4qx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qx4_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4qx4_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4qx4_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 4qx4_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/4qx4 ftp://data.pdbj.org/pub/pdb/validation_reports/qx/4qx4 | HTTPS FTP |
-Related structure data
Related structure data | 2duxS 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: 35898.340 Da / Num. of mol.: 1 / Fragment: Human Aldose Reductase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: P15121, aldose reductase | ||
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#2: Chemical | ChemComp-NAP / | ||
#3: Chemical | #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: 2.18 Å3/Da / Density % sol: 43.67 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50 mM di-Ammoniumhydrogen citrate pH 5.0 PEG6000= 5 % (m/V) DTT= 5.15 g/L NADP+= 0.66 g/L and Human Aldose Reductase= 15 mg/ml. Afterwards the crystals were soaked into Tris 100 mM 25% (m/V) ...Details: 50 mM di-Ammoniumhydrogen citrate pH 5.0 PEG6000= 5 % (m/V) DTT= 5.15 g/L NADP+= 0.66 g/L and Human Aldose Reductase= 15 mg/ml. Afterwards the crystals were soaked into Tris 100 mM 25% (m/V) PEG6000 pH 8.0 saturated with the inhibitor. The well solution for crystallization was 120mM di-Ammonium hydrogen citrate with 20% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2013 / Details: Silicon, active surface 50 nm Rh-coated |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→50 Å / Num. all: 79172 / Num. obs: 79172 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 8.461 Å2 / Rsym value: 0.051 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.26→1.28 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 3759 / Rsym value: 0.3 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2DUX Resolution: 1.259→17.841 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.259→17.841 Å
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Refine LS restraints |
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LS refinement shell |
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