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Yorodumi- PDB-5ouk: Crystal structure of human AKR1B1 complexed with NADP+ and compound 41 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ouk | |||||||||
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Title | Crystal structure of human AKR1B1 complexed with NADP+ and compound 41 | |||||||||
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: 0.959 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 | 5ouk.cif.gz | 170.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ouk.ent.gz | 134.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ouk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ouk_validation.pdf.gz | 976.3 KB | Display | wwPDB validaton report |
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Full document | 5ouk_full_validation.pdf.gz | 978.2 KB | Display | |
Data in XML | 5ouk_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 5ouk_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/5ouk ftp://data.pdbj.org/pub/pdb/validation_reports/ou/5ouk | HTTPS FTP |
-Related structure data
Related structure data | 5ou0C 5oujC 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-AVT / |
#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: 2.22 Å3/Da / Density % sol: 44.52 % |
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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→21.55 Å / Num. obs: 171622 / % possible obs: 91 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 36.4 |
Reflection shell | Resolution: 0.96→0.99 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 4.03 / Num. unique obs: 13444 / % possible all: 72.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IGS Resolution: 0.959→24.144 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 13.29 / 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: 0.959→24.144 Å
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Refine LS restraints |
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LS refinement shell |
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