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- PDB-9uj1: Crystal Structure of AKR1C3 in Complex with an Osthole-Derived In... -

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Entry
Database: PDB / ID: 9uj1
TitleCrystal Structure of AKR1C3 in Complex with an Osthole-Derived Inhibitor
ComponentsAldo-keto reductase family 1 member C3
KeywordsOXIDOREDUCTASE / AKR1C3 / 17 beta-HSD5 / Osthole / Inhibitor / Complex
Function / homology
Function and homology information


prostaglandin-F synthase / testosterone 17beta-dehydrogenase (NADP+) / cellular response to prostaglandin stimulus / cellular response to corticosteroid stimulus / prostaglandin F synthase activity / macromolecule metabolic process / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / prostaglandin D2 11-ketoreductase activity / ketoreductase activity / negative regulation of retinoic acid biosynthetic process ...prostaglandin-F synthase / testosterone 17beta-dehydrogenase (NADP+) / cellular response to prostaglandin stimulus / cellular response to corticosteroid stimulus / prostaglandin F synthase activity / macromolecule metabolic process / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / prostaglandin D2 11-ketoreductase activity / ketoreductase activity / negative regulation of retinoic acid biosynthetic process / 5-alpha-androstane-3-beta,17-beta-diol dehydrogenase (NADP+) activity / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity / farnesol catabolic process / 3alpha-hydroxysteroid 3-dehydrogenase / cellular response to jasmonic acid stimulus / Delta4-3-oxosteroid 5beta-reductase activity / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / : / testosterone dehydrogenase (NADP+) activity / 3-alpha-hydroxysteroid 3-dehydrogenase [NAD(P)+] activity / androsterone dehydrogenase [NAD(P)+] activity / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / RA biosynthesis pathway / regulation of testosterone biosynthetic process / ketosteroid monooxygenase activity / testosterone biosynthetic process / androstan-3-alpha,17-beta-diol dehydrogenase (NAD+) activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / testosterone dehydrogenase (NAD+) activity / regulation of retinoic acid receptor signaling pathway / cellular response to prostaglandin D stimulus / prostanoid biosynthetic process / progesterone metabolic process / 17beta-estradiol 17-dehydrogenase / retinal metabolic process / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) activity / 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 / bile acid binding / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase (NAD+) activity / aldose reductase (NADPH) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / prostaglandin metabolic process / renal absorption / steroid metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of endothelial cell apoptotic process / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / retinoid metabolic process / Retinoid metabolism and transport / keratinocyte differentiation / response to nutrient / cellular response to calcium ion / cellular response to starvation / 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 / cytoplasm / cytosol
Similarity search - Function
Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / 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
Similarity search - Domain/homology
: / 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: 2.15 Å
AuthorsLiu, H. / Zheng, X. / Sun, M.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: Crystal Structure of AKR1C3 in Complex with an Osthole-Derived Inhibitor
Authors: Liu, H. / Sun, M.
History
DepositionApr 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldo-keto reductase family 1 member C3
B: Aldo-keto reductase family 1 member C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0146
Polymers73,8122
Non-polymers2,2024
Water2,522140
1
A: Aldo-keto reductase family 1 member C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0073
Polymers36,9061
Non-polymers1,1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-3 kcal/mol
Surface area13090 Å2
MethodPISA
2
B: Aldo-keto reductase family 1 member C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0073
Polymers36,9061
Non-polymers1,1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-4 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.678, 87.665, 75.546
Angle α, β, γ (deg.)90.000, 102.541, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#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 / Prostaglandin F synthase / PGFS / Testosterone 17-beta-dehydrogenase 5


Mass: 36906.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C3, DDH1, HSD17B5, KIAA0119, PGFS / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P42330, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, 3beta(or 20alpha)-hydroxysteroid dehydrogenase, 3alpha(or 20beta)-hydroxysteroid ...References: UniProt: P42330, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, 3beta(or 20alpha)-hydroxysteroid dehydrogenase, 3alpha(or 20beta)-hydroxysteroid dehydrogenase, 17beta-estradiol 17-dehydrogenase, 3alpha-hydroxysteroid 3-dehydrogenase, prostaglandin-F synthase, 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+), testosterone 17beta-dehydrogenase (NADP+)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1EPD / (~{E})-4-(7-methoxy-2-oxidanylidene-chromen-8-yl)-2-methyl-~{N},~{N}-dipropyl-but-2-enamide


Mass: 357.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 277 K / Method: evaporation / Details: 15%~18% PEG8000, 140 mM NaCl, 100 mM MES (PH 6.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.15→23.33 Å / Num. obs: 33757 / % possible obs: 99.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 21.85 Å2 / CC1/2: 0.993 / Net I/σ(I): 9.24
Reflection shellResolution: 2.15→2.23 Å / Num. unique obs: 3382 / CC1/2: 0.891

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Processing

Software
NameVersionClassification
PHENIXdev.5306refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→23.33 Å / SU ML: 0.2686 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.1207
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2431 2000 5.93 %
Rwork0.1886 31730 -
obs0.1918 33730 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.89 Å2
Refinement stepCycle: LAST / Resolution: 2.15→23.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4944 0 148 140 5232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075215
X-RAY DIFFRACTIONf_angle_d0.84557091
X-RAY DIFFRACTIONf_chiral_restr0.0498774
X-RAY DIFFRACTIONf_plane_restr0.0075942
X-RAY DIFFRACTIONf_dihedral_angle_d17.39392057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.29591410.24532248X-RAY DIFFRACTION99.87
2.2-2.260.29911430.23132246X-RAY DIFFRACTION100
2.26-2.330.28241440.2132294X-RAY DIFFRACTION99.96
2.33-2.40.29511410.21722234X-RAY DIFFRACTION100
2.4-2.490.27041410.21332243X-RAY DIFFRACTION100
2.49-2.590.28061430.2082270X-RAY DIFFRACTION99.92
2.59-2.710.28341440.19682275X-RAY DIFFRACTION100
2.71-2.850.24711420.19532246X-RAY DIFFRACTION99.92
2.85-3.030.25071430.19452282X-RAY DIFFRACTION100
3.03-3.260.25321420.18522255X-RAY DIFFRACTION99.96
3.26-3.590.2121430.18062264X-RAY DIFFRACTION99.96
3.59-4.110.21171440.16852279X-RAY DIFFRACTION99.96
4.11-5.160.2211430.15922271X-RAY DIFFRACTION99.83
5.17-23.330.19241460.16852323X-RAY DIFFRACTION99.8

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