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- PDB-4fa3: Crystal structure of human 17beta-hydroxysteroid dehydrogenase ty... -

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Basic information

Entry
Database: PDB / ID: 4fa3
TitleCrystal structure of human 17beta-hydroxysteroid dehydrogenase type 5 in complex with (R)-1-(naphthalen-2-ylsulfonyl)piperidine-3-carboxylic acid (86)
ComponentsAldo-keto reductase family 1 member C3
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / TIM-barrel / aldo-keto reductase / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex
Function / homology
Function and homology information


prostaglandin-F synthase / testosterone 17beta-dehydrogenase (NADP+) / prostaglandin D2 11-ketoreductase activity / ketoreductase activity / prostaglandin F synthase activity / cellular response to prostaglandin stimulus / cellular response to corticosteroid stimulus / macromolecule metabolic process / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity / 3beta(or 20alpha)-hydroxysteroid dehydrogenase ...prostaglandin-F synthase / testosterone 17beta-dehydrogenase (NADP+) / prostaglandin D2 11-ketoreductase activity / ketoreductase activity / prostaglandin F synthase activity / cellular response to prostaglandin stimulus / cellular response to corticosteroid stimulus / macromolecule metabolic process / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / negative regulation of retinoic acid biosynthetic process / 5alpha-androstane-3beta,17beta-diol dehydrogenase activity / Delta4-3-oxosteroid 5beta-reductase activity / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / farnesol catabolic process / geranylgeranyl reductase activity / 3alpha-hydroxysteroid 3-dehydrogenase / cellular response to jasmonic acid stimulus / regulation of testosterone biosynthetic process / : / androsterone dehydrogenase activity / testosterone biosynthetic process / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / RA biosynthesis pathway / testosterone dehydrogenase (NAD+) activity / cellular response to prostaglandin D stimulus / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / ketosteroid monooxygenase activity / regulation of retinoic acid receptor signaling pathway / retinal metabolic process / testosterone 17-beta-dehydrogenase (NADP+) activity / progesterone metabolic process / 17beta-estradiol 17-dehydrogenase / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / aldo-keto reductase (NADPH) activity / all-trans-retinol dehydrogenase (NAD+) activity / cyclooxygenase pathway / positive regulation of endothelial cell apoptotic process / prostaglandin H2 endoperoxidase reductase activity / all-trans-retinol dehydrogenase (NADP+) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / daunorubicin metabolic process / doxorubicin metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / retinal dehydrogenase activity / bile acid binding / aldose reductase (NADPH) activity / retinoid metabolic process / prostaglandin metabolic process / renal absorption / steroid metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Retinoid metabolism and transport / keratinocyte differentiation / cellular response to starvation / cellular response to calcium ion / response to nutrient / male gonad development / positive regulation of reactive oxygen species metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
Aldo-keto reductase family 1 member C / 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 ...Aldo-keto reductase family 1 member C / 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-0SL / ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member C3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTurnbull, A.P. / Jamieson, S.M.F. / Brooke, D.G. / Heinrich, D. / Atwell, G.J. / Silva, S. / Hamilton, E.J. / Rigoreau, L.J.M. / Trivier, E. / Soudy, C. ...Turnbull, A.P. / Jamieson, S.M.F. / Brooke, D.G. / Heinrich, D. / Atwell, G.J. / Silva, S. / Hamilton, E.J. / Rigoreau, L.J.M. / Trivier, E. / Soudy, C. / Samlal, S.S. / Owen, P.J. / Schroeder, E. / Raynham, T. / Flanagan, J.U. / Denny, W.A.
CitationJournal: J.Med.Chem. / Year: 2012
Title: 3-(3,4-Dihydroisoquinolin-2(1H)-ylsulfonyl)benzoic acids; a New Class of Highly Potent and Selective Inhibitors of the Type 5 17-beta-hydroxysteroid Dehydrogenase AKR1C3
Authors: Jamieson, S.M. / Brooke, D.G. / Heinrich, D. / Atwell, G.J. / Silva, S. / Hamilton, E.J. / Turnbull, A.P. / Rigoreau, L.J. / Trivier, E. / Soudy, C. / Samlal, S.S. / Owen, P.J. / Schroeder, ...Authors: Jamieson, S.M. / Brooke, D.G. / Heinrich, D. / Atwell, G.J. / Silva, S. / Hamilton, E.J. / Turnbull, A.P. / Rigoreau, L.J. / Trivier, E. / Soudy, C. / Samlal, S.S. / Owen, P.J. / Schroeder, E. / Raynham, T. / Flanagan, J.U. / Denny, W.A.
History
DepositionMay 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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: Aldo-keto reductase family 1 member C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1615
Polymers37,9771
Non-polymers1,1844
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.127, 63.469, 96.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aldo-keto reductase family 1 member C3 / 17-beta-hydroxysteroid dehydrogenase type 5 / 17-beta-HSD 5 / 3-alpha-HSD type II / brain / 3-alpha- ...17-beta-hydroxysteroid dehydrogenase type 5 / 17-beta-HSD 5 / 3-alpha-HSD type II / brain / 3-alpha-hydroxysteroid dehydrogenase type 2 / 3-alpha-HSD type 2 / Chlordecone reductase homolog HAKRb / Dihydrodiol dehydrogenase 3 / DD-3 / DD3 / Dihydrodiol dehydrogenase type I / HA1753 / Indanol dehydrogenase / Prostaglandin F synthase / PGFS / Testosterone 17-beta-dehydrogenase 5 / Trans-1 / 2-dihydrobenzene-1 / 2-diol dehydrogenase


Mass: 37977.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C3, DDH1, HSD17B5, KIAA0119, PGFS / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: P42330, Oxidoreductases, EC: 1.1.1.213, indanol dehydrogenase, prostaglandin-F synthase, EC: 1.1.1.63, testosterone 17beta-dehydrogenase (NADP+), trans-1,2-dihydrobenzene-1,2-diol dehydrogenase

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Non-polymers , 5 types, 107 molecules

#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-0SL / (3R)-1-(naphthalen-2-ylsulfonyl)piperidine-3-carboxylic acid


Mass: 319.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17NO4S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.2 M sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54182 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 31, 2010 / Details: Varimax HF Optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54182 Å / Relative weight: 1
ReflectionResolution: 2.2→18.68 Å / Num. all: 17915 / Num. obs: 17915 / % possible obs: 97.6 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.096
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1656 / % possible all: 93.5

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0072refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FGB

2fgb


Resolution: 2.2→18.68 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.906 / SU B: 5.898 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27808 915 5.1 %RANDOM
Rwork0.20772 ---
obs0.21115 17000 97.43 %-
all-51579 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.701 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å20 Å2
2---0.63 Å20 Å2
3---1.72 Å2
Refinement stepCycle: LAST / Resolution: 2.2→18.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2414 0 78 103 2595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222556
X-RAY DIFFRACTIONr_bond_other_d0.0010.021738
X-RAY DIFFRACTIONr_angle_refined_deg1.8482.0023475
X-RAY DIFFRACTIONr_angle_other_deg1.0453.0044187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7935305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.90124.159113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.74815424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.281514
X-RAY DIFFRACTIONr_chiral_restr0.120.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212785
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02499
X-RAY DIFFRACTIONr_mcbond_it0.9061.51533
X-RAY DIFFRACTIONr_mcbond_other0.2611.5606
X-RAY DIFFRACTIONr_mcangle_it1.57822472
X-RAY DIFFRACTIONr_scbond_it2.57131023
X-RAY DIFFRACTIONr_scangle_it3.7244.51002
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 72 -
Rwork0.247 1161 -
obs-915 93.98 %

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