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- PDB-4prr: Human Aldose Reductase complexed with Schl7815 ((3-[3-(5-NITROFUR... -

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Basic information

Entry
Database: PDB / ID: 4prr
TitleHuman Aldose Reductase complexed with Schl7815 ((3-[3-(5-NITROFURAN-2-YL)PHENYL]PROPANOIC ACID)at 1.01 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 / 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
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
3-[3-(5-nitrofuran-2-yl)phenyl]propanoic acid / 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: 1.01 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)36,7723
Polymers35,7671
Non-polymers1,0052
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.305, 66.863, 47.214
Angle α, β, γ (deg.)90.00, 92.54, 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: 35767.145 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


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-2W9 / 3-[3-(5-nitrofuran-2-yl)phenyl]propanoic acid


Mass: 261.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11NO5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer 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: 43.41 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: di-Ammoniumhydrogen citrate pH 5.0, PEG6000= 5 % (m/V), DTT= 5.15 g/L, ADP= 0,66 g/L, protein 15 mg/ml. Soaking conditions: Tris buffer, Tris 100 mM 25 %(m/V) PEG6000 pH 8.0 saturated with ...Details: di-Ammoniumhydrogen citrate pH 5.0, PEG6000= 5 % (m/V), DTT= 5.15 g/L, ADP= 0,66 g/L, protein 15 mg/ml. Soaking conditions: Tris buffer, Tris 100 mM 25 %(m/V) PEG6000 pH 8.0 saturated with the inhibitor, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 2013 / Details: Silicon, active surace 50 nm Rh-coated
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.01→50 Å / Num. all: 148147 / Num. obs: 148147 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 7.483 Å2 / Rsym value: 0.056 / Net I/σ(I): 16.85
Reflection shellResolution: 1.01→1.03 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.04 / Num. unique all: 7006 / Rsym value: 0.421 / % possible all: 87.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DUX

2dux


Resolution: 1.01→18.776 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 13.67 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.155 7408 5 %RANDOM
Rwork0.1437 ---
obs0.1443 148093 92.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.01→18.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 67 334 2871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062719
X-RAY DIFFRACTIONf_angle_d1.2533731
X-RAY DIFFRACTIONf_dihedral_angle_d13.9521018
X-RAY DIFFRACTIONf_chiral_restr0.078416
X-RAY DIFFRACTIONf_plane_restr0.007478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0092-1.02060.26591790.22564152X-RAY DIFFRACTION82
1.0206-1.03260.23682340.20384422X-RAY DIFFRACTION87
1.0326-1.04520.23552400.19284473X-RAY DIFFRACTION88
1.0452-1.05850.20482290.17434490X-RAY DIFFRACTION89
1.0585-1.07240.18582320.16054574X-RAY DIFFRACTION89
1.0724-1.08710.16732380.15844508X-RAY DIFFRACTION90
1.0871-1.10260.16992300.14724627X-RAY DIFFRACTION91
1.1026-1.11910.15792430.14284624X-RAY DIFFRACTION91
1.1191-1.13660.14622380.13154665X-RAY DIFFRACTION92
1.1366-1.15520.13552510.12764607X-RAY DIFFRACTION92
1.1552-1.17510.13222610.12064595X-RAY DIFFRACTION91
1.1751-1.19650.1312420.12024667X-RAY DIFFRACTION92
1.1965-1.21950.15112270.12154716X-RAY DIFFRACTION93
1.2195-1.24440.13622560.11834682X-RAY DIFFRACTION92
1.2444-1.27140.13462330.11784684X-RAY DIFFRACTION92
1.2714-1.3010.13912560.11724692X-RAY DIFFRACTION93
1.301-1.33350.14542780.11744707X-RAY DIFFRACTION93
1.3335-1.36960.13532640.11554753X-RAY DIFFRACTION94
1.3696-1.40980.12122600.1154751X-RAY DIFFRACTION94
1.4098-1.45530.13172450.124792X-RAY DIFFRACTION94
1.4553-1.50730.12712520.12394759X-RAY DIFFRACTION94
1.5073-1.56760.14552530.1274799X-RAY DIFFRACTION94
1.5676-1.6390.13632640.1314745X-RAY DIFFRACTION94
1.639-1.72530.14682460.13834804X-RAY DIFFRACTION95
1.7253-1.83330.16652530.14954847X-RAY DIFFRACTION95
1.8333-1.97470.16022610.15094909X-RAY DIFFRACTION96
1.9747-2.17320.14442550.14514866X-RAY DIFFRACTION96
2.1732-2.4870.16062540.1534994X-RAY DIFFRACTION97
2.487-3.1310.17962720.16075006X-RAY DIFFRACTION98
3.131-18.7790.15672620.15764775X-RAY DIFFRACTION92

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