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- PDB-8jp2: Crystal structure of AKR1C1 in complex with DFV -

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Basic information

Entry
Database: PDB / ID: 8jp2
TitleCrystal structure of AKR1C1 in complex with DFV
ComponentsAldo-keto reductase family 1 member C1
KeywordsOXIDOREDUCTASE / Aldo-Keto Reductase 1C1 / 20alpha-hydroxysteroid dehydrogenase / Complex / Inhibitor / Flavanone
Function / homology
Function and homology information


3-beta-hydroxy-5-beta-steroid dehydrogenase (NADP+) activity / 20alpha-hydroxysteroid dehydrogenase / 17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase [NAD(P)+] activity / : / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / 3(or 17)alpha-hydroxysteroid dehydrogenase / 3(or 17)beta-hydroxysteroid dehydrogenase ...3-beta-hydroxy-5-beta-steroid dehydrogenase (NADP+) activity / 20alpha-hydroxysteroid dehydrogenase / 17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase [NAD(P)+] activity / : / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / 3(or 17)alpha-hydroxysteroid dehydrogenase / 3(or 17)beta-hydroxysteroid dehydrogenase / indanol dehydrogenase activity / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / 5-alpha-androstane-3-beta,17-beta-diol dehydrogenase (NADP+) activity / 3alpha-hydroxysteroid 3-dehydrogenase / cellular response to jasmonic acid stimulus / androsterone dehydrogenase [NAD(P)+] activity / testosterone dehydrogenase (NADP+) activity / ketosteroid monooxygenase activity / intestinal cholesterol absorption / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase (NAD+) activity / retinal metabolic process / progesterone metabolic process / 17beta-estradiol 17-dehydrogenase / carboxylic acid binding / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / : / bile acid metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / daunorubicin metabolic process / doxorubicin metabolic process / bile acid binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / aldose reductase (NADPH) activity / Prednisone ADME / prostaglandin metabolic process / bile acid and bile salt transport / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / retinoid metabolic process / Retinoid metabolism and transport / digestion / epithelial cell differentiation / xenobiotic metabolic process / cholesterol homeostasis / positive regulation of reactive oxygen species metabolic process / extracellular exosome / 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
7-HYDROXY-2-(4-HYDROXY-PHENYL)-CHROMAN-4-ONE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member C1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsZheng, X.H. / Liu, H. / Yao, Z.Q. / Zhang, L.P.
Funding support1items
OrganizationGrant numberCountry
Other government2022A1515010040
CitationJournal: Chem.Biol.Interact. / Year: 2023
Title: Inhibition of AKR1Cs by liquiritigenin and the structural basis.
Authors: Liu, H. / Yao, Z. / Sun, M. / Zhang, C. / Huang, Y.Y. / Luo, H.B. / Wu, D. / Zheng, X.
History
DepositionJun 10, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 24, 2024Provider: 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 C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8393
Polymers36,8391
Non-polymers1,0002
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-4 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.462, 83.837, 49.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aldo-keto reductase family 1 member C1 / 20-alpha-hydroxysteroid dehydrogenase / 20-alpha-HSD / Chlordecone reductase homolog HAKRC / ...20-alpha-hydroxysteroid dehydrogenase / 20-alpha-HSD / Chlordecone reductase homolog HAKRC / Dihydrodiol dehydrogenase 1 / DD1 / High-affinity hepatic bile acid-binding protein / HBAB


Mass: 36839.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C1, DDH, DDH1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q04828, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, indanol dehydrogenase, 3(or 17)alpha-hydroxysteroid dehydrogenase, 3beta(or 20alpha)- ...References: UniProt: Q04828, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, indanol dehydrogenase, 3(or 17)alpha-hydroxysteroid dehydrogenase, 3beta(or 20alpha)-hydroxysteroid dehydrogenase, 3alpha-hydroxysteroid 3-dehydrogenase, 3(or 17)beta-hydroxysteroid dehydrogenase, 3alpha(or 20beta)-hydroxysteroid dehydrogenase, 17beta-estradiol 17-dehydrogenase, trans-1,2-dihydrobenzene-1,2-diol dehydrogenase, 20alpha-hydroxysteroid dehydrogenase
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DFV / 7-HYDROXY-2-(4-HYDROXY-PHENYL)-CHROMAN-4-ONE / 5-DEOXYFLAVANONE


Mass: 256.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: agonist*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 44.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 23-27% (w/v) PEG 4000, 100 mM Hepes , 10 mM CaCl2 and 0.4 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.8→21.23 Å / Num. obs: 29670 / % possible obs: 99.6 % / Redundancy: 2 % / Biso Wilson estimate: 10.76 Å2 / CC1/2: 0.939 / Rmerge(I) obs: 0.106 / Net I/σ(I): 10.5
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 2944 / CC1/2: 0.858 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(dev_3283: ???)refinement
CrysalisProdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→12.777 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2491 1521 5.28 %
Rwork0.1965 --
obs0.1991 28787 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→12.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 0 67 443 3065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072687
X-RAY DIFFRACTIONf_angle_d0.9263653
X-RAY DIFFRACTIONf_dihedral_angle_d8.3041654
X-RAY DIFFRACTIONf_chiral_restr0.056399
X-RAY DIFFRACTIONf_plane_restr0.007504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.85790.27951360.22342355X-RAY DIFFRACTION93
1.8579-1.92410.30581690.22462394X-RAY DIFFRACTION97
1.9241-2.00090.25451510.21442413X-RAY DIFFRACTION96
2.0009-2.09160.31071310.20872485X-RAY DIFFRACTION97
2.0916-2.20130.27261410.20052469X-RAY DIFFRACTION97
2.2013-2.33850.24621270.20662455X-RAY DIFFRACTION97
2.3385-2.51770.26281440.20412462X-RAY DIFFRACTION98
2.5177-2.76880.27551340.19852529X-RAY DIFFRACTION100
2.7688-3.16410.24341280.19822541X-RAY DIFFRACTION100
3.1641-3.96660.21471210.17232594X-RAY DIFFRACTION100
3.9666-12.7770.19581390.18292569X-RAY DIFFRACTION99

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