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- PDB-4prt: Human Aldose Reductase complexed with Schl12221 ({2-[5-(3-NITROPH... -

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Basic information

Entry
Database: PDB / ID: 4prt
TitleHuman Aldose Reductase complexed with Schl12221 ({2-[5-(3-NITROPHENYL)FURAN-2-YL]PHENYL}ACETIC ACID) at 0.96 A
ComponentsAldose reductase
KeywordsOxidoreductase/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 / 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
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-2WB / 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
AuthorsRechlin, C. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Keys to open the specificity pocket: Biphenylic Inhibitors of the human aldose reductase
Authors: Rechlin, C. / Heine, A. / Ortmann, R. / Schlitzer, M. / Klebe, G.
History
DepositionMar 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)36,9653
Polymers35,8981
Non-polymers1,0672
Water7,422412
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.320, 66.972, 47.308
Angle α, β, γ (deg.)90.00, 92.52, 90.00
Int Tables number4
Space group name H-MP1211

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


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-2WB / {2-[5-(3-nitrophenyl)furan-2-yl]phenyl}acetic acid


Mass: 323.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H13NO5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE INDICATED THAT THE SEQUENCING RESULT OF THE PLASMID SHOWED A ILE IN POSITION 4

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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: 2.17 Å3/Da / Density % sol: 43.43 %
Crystal growTemperature: 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, Human Aldose Reductase= 15 mg/ml. Afterwards the crystals have been soaked into Tris buffer, ...Details: 50 mM di-Ammoniumhydrogen citrate pH 5.0, PEG6000= 5 % (m/V), DTT= 5,15 g/L, NADP+= 0,66 g/L, Human Aldose Reductase= 15 mg/ml. Afterwards the crystals have been soaked into Tris buffer, Tris 100 mM 25% (m/V) PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2014 / Details: Silicon, active surface 50 nm Rh- coated
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 0.96→50 Å / Num. all: 185561 / Num. obs: 185561 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.49 % / Biso Wilson estimate: 6.918 Å2 / Rsym value: 0.034 / Net I/σ(I): 19.44
Reflection shellResolution: 0.96→1.02 Å / Redundancy: 3.13 % / Mean I/σ(I) obs: 2.82 / Num. unique all: 29443 / Rsym value: 0.409 / % possible all: 97.6

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2DUX

2dux


Resolution: 0.96→33.486 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 11.18 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1366 9277 5 %RANDOM
Rwork0.126 ---
obs0.1265 185558 99.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.96→33.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2504 0 72 412 2988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062827
X-RAY DIFFRACTIONf_angle_d1.313883
X-RAY DIFFRACTIONf_dihedral_angle_d15.1881070
X-RAY DIFFRACTIONf_chiral_restr0.082431
X-RAY DIFFRACTIONf_plane_restr0.007500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9599-0.97080.23832970.20755645X-RAY DIFFRACTION95
0.9708-0.98220.18743040.19365786X-RAY DIFFRACTION98
0.9822-0.99420.17683050.17765783X-RAY DIFFRACTION98
0.9942-1.00680.16493070.17285838X-RAY DIFFRACTION98
1.0068-1.02010.19743010.1655733X-RAY DIFFRACTION98
1.0201-1.0340.16423070.15675831X-RAY DIFFRACTION99
1.034-1.04880.15213090.14245867X-RAY DIFFRACTION99
1.0488-1.06450.14163090.12475869X-RAY DIFFRACTION100
1.0645-1.08110.13133100.11885883X-RAY DIFFRACTION100
1.0811-1.09880.1273090.11355878X-RAY DIFFRACTION100
1.0988-1.11780.11623080.10715849X-RAY DIFFRACTION100
1.1178-1.13810.11153120.10475930X-RAY DIFFRACTION100
1.1381-1.160.11883080.10015849X-RAY DIFFRACTION99
1.16-1.18370.10193120.10035922X-RAY DIFFRACTION100
1.1837-1.20940.11783100.10275891X-RAY DIFFRACTION100
1.2094-1.23750.11373090.10145875X-RAY DIFFRACTION100
1.2375-1.26850.11953100.10545893X-RAY DIFFRACTION100
1.2685-1.30280.12593100.10355895X-RAY DIFFRACTION100
1.3028-1.34110.12213120.1095924X-RAY DIFFRACTION100
1.3411-1.38440.13033090.10855868X-RAY DIFFRACTION100
1.3844-1.43390.1183120.1115930X-RAY DIFFRACTION100
1.4339-1.49130.12853110.10845904X-RAY DIFFRACTION100
1.4913-1.55920.11353100.10845893X-RAY DIFFRACTION100
1.5592-1.64140.11983120.11275934X-RAY DIFFRACTION100
1.6414-1.74420.13933100.12215893X-RAY DIFFRACTION100
1.7442-1.87890.13523110.12965907X-RAY DIFFRACTION100
1.8789-2.06790.14263120.13455919X-RAY DIFFRACTION100
2.0679-2.36710.14253120.1375932X-RAY DIFFRACTION100
2.3671-2.9820.15823120.14495928X-RAY DIFFRACTION100
2.982-33.50640.13943170.1316032X-RAY DIFFRACTION100

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