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Yorodumi- PDB-5ouj: Crystal structure of human AKR1B1 complexed with NADP+ and compound 39 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ouj | ||||||
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Title | Crystal structure of human AKR1B1 complexed with NADP+ and compound 39 | ||||||
Components | Aldose reductase | ||||||
Keywords | OXIDOREDUCTASE / alpha-beta TIM barrel / cytosol / aldo-keto reductase / pyrimido[4 / 5-c]quinolone-2-acetic acid scaffold | ||||||
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: 0.96 Å | ||||||
Authors | Cousido-Siah, A. / Ruiz, F.X. / Mitschler, A. / Metwally, K. / Podjarny, A. | ||||||
Citation | Journal: Eur J Med Chem / Year: 2018 Title: Design, synthesis, structure-activity relationships and X-ray structural studies of novel 1-oxopyrimido[4,5-c]quinoline-2-acetic acid derivatives as selective and potent inhibitors of human aldose reductase. Authors: Crespo, I. / Gimenez-Dejoz, J. / Porte, S. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Pratsinis, H. / Kletsas, D. / Pares, X. / Ruiz, F.X. / Metwally, K. / Farres, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ouj.cif.gz | 166.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ouj.ent.gz | 129.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ouj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ouj_validation.pdf.gz | 998.5 KB | Display | wwPDB validaton report |
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Full document | 5ouj_full_validation.pdf.gz | 1001.1 KB | Display | |
Data in XML | 5ouj_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 5ouj_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/5ouj ftp://data.pdbj.org/pub/pdb/validation_reports/ou/5ouj | HTTPS FTP |
-Related structure data
Related structure data | 5ou0C 5oukC 4igsS 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: 35898.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P15121, aldose reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-AW8 / |
#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: 2.2 Å3/Da / Density % sol: 44.18 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% PEG 6000, 50 mM MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 3, 2014 |
Radiation | Monochromator: Bartels monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 0.96→28.9 Å / Num. obs: 173015 / % possible obs: 92.5 % / Redundancy: 3.3 % / Rrim(I) all: 0.022 / Net I/σ(I): 48.21 |
Reflection shell | Resolution: 0.96→0.99 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 3.43 / Num. unique obs: 14408 / Rrim(I) all: 0.27 / % possible all: 77.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IGS Resolution: 0.96→28.9 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.76 / Phase error: 12.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.96→28.9 Å
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Refine LS restraints |
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LS refinement shell |
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