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- PDB-5ouj: Crystal structure of human AKR1B1 complexed with NADP+ and compound 39 -

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Basic information

Entry
Database: PDB / ID: 5ouj
TitleCrystal structure of human AKR1B1 complexed with NADP+ and compound 39
ComponentsAldose reductase
KeywordsOXIDOREDUCTASE / 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 / aldose reductase / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / C21-steroid hormone biosynthetic process / NADP-retinol dehydrogenase / Pregnenolone biosynthesis ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / aldose reductase / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / C21-steroid hormone biosynthetic process / NADP-retinol dehydrogenase / Pregnenolone biosynthesis / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / metanephric collecting duct development / all-trans-retinol dehydrogenase (NADP+) activity / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase (NAD+) activity / aldose reductase (NADPH) activity / epithelial cell maturation / cellular hyperosmotic salinity response / retinoid metabolic process / renal water homeostasis / carbohydrate metabolic process / electron transfer activity / negative regulation of apoptotic process / mitochondrion / extracellular space / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel ...Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-AW8 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsCousido-Siah, A. / Ruiz, F.X. / Mitschler, A. / Metwally, K. / Podjarny, A.
CitationJournal: 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
DepositionAug 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0423
Polymers35,8981
Non-polymers1,1432
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-5 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.050, 46.979, 47.283
Angle α, β, γ (deg.)76.40, 67.57, 77.40
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Aldose reductase / AR / Aldehyde reductase / Aldo-keto reductase family 1 member B1


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
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-AW8 / 2-[(1~{R})-5-(4-chlorophenyl)-9-fluoranyl-3-methyl-1-oxidanyl-1~{H}-pyrimido[4,5-c]quinolin-2-yl]ethanoic acid


Mass: 399.803 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15ClFN3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 3, 2014
RadiationMonochromator: Bartels monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IGS

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
RfactorNum. reflection% reflection
Rfree0.1465 -5 %
Rwork0.1299 --
obs0.1307 173015 92.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.96→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 76 368 2969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182833
X-RAY DIFFRACTIONf_angle_d1.7333903
X-RAY DIFFRACTIONf_dihedral_angle_d16.9811105
X-RAY DIFFRACTIONf_chiral_restr0.167433
X-RAY DIFFRACTIONf_plane_restr0.012498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9603-0.97120.20694000.19918062X-RAY DIFFRACTION69
0.9712-0.98260.20195200.18429182X-RAY DIFFRACTION78
0.9826-0.99460.19875380.17210088X-RAY DIFFRACTION85
0.9946-1.00720.16686480.155310470X-RAY DIFFRACTION89
1.0072-1.02050.16885800.145710720X-RAY DIFFRACTION91
1.0205-1.03450.14535580.13110762X-RAY DIFFRACTION91
1.0345-1.04920.14715140.127910948X-RAY DIFFRACTION92
1.0492-1.06490.1435900.123110962X-RAY DIFFRACTION92
1.0649-1.08150.13275640.117310962X-RAY DIFFRACTION93
1.0815-1.09930.12916000.113510984X-RAY DIFFRACTION93
1.0993-1.11820.12066600.106510986X-RAY DIFFRACTION93
1.1182-1.13860.13695480.103711004X-RAY DIFFRACTION93
1.1386-1.16050.12925420.102411044X-RAY DIFFRACTION93
1.1605-1.18410.11725580.100711172X-RAY DIFFRACTION94
1.1841-1.20990.11545780.101511204X-RAY DIFFRACTION94
1.2099-1.2380.12815800.102811140X-RAY DIFFRACTION94
1.238-1.2690.11676400.099811150X-RAY DIFFRACTION94
1.269-1.30330.13185500.101911214X-RAY DIFFRACTION95
1.3033-1.34170.12145960.102411248X-RAY DIFFRACTION95
1.3417-1.3850.12266160.104811334X-RAY DIFFRACTION95
1.385-1.43450.12015880.106511308X-RAY DIFFRACTION95
1.4345-1.49190.12866360.103211330X-RAY DIFFRACTION96
1.4919-1.55980.11915820.104711366X-RAY DIFFRACTION96
1.5598-1.6420.12766340.110511504X-RAY DIFFRACTION97
1.642-1.74490.13875680.120111626X-RAY DIFFRACTION97
1.7449-1.87960.14486360.130711522X-RAY DIFFRACTION97
1.8796-2.06870.1565600.137811552X-RAY DIFFRACTION98
2.0687-2.3680.15475820.14711600X-RAY DIFFRACTION97
2.368-2.98310.1816200.160611306X-RAY DIFFRACTION96
2.9831-31.85580.15745680.145310856X-RAY DIFFRACTION92

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