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- PDB-9kpi: Aromatic acetyl piperidine derivatives as soluble epoxide hydrola... -

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Basic information

Entry
Database: PDB / ID: 9kpi
TitleAromatic acetyl piperidine derivatives as soluble epoxide hydrolase inhibitor
ComponentsBifunctional epoxide hydrolase 2
KeywordsHYDROLASE / sEH / inhibition / complex
Function / homology
Function and homology information


lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / phospholipid dephosphorylation / lipid phosphatase activity / Biosynthesis of maresins / epoxide metabolic process / lysophosphatidic acid phosphatase activity / soluble epoxide hydrolase / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) ...lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / phospholipid dephosphorylation / lipid phosphatase activity / Biosynthesis of maresins / epoxide metabolic process / lysophosphatidic acid phosphatase activity / soluble epoxide hydrolase / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / epoxide hydrolase activity / dephosphorylation / regulation of cholesterol metabolic process / phosphatase activity / peroxisomal matrix / toxic substance binding / cholesterol homeostasis / Peroxisomal protein import / regulation of cell growth / response to toxic substance / peroxisome / positive regulation of gene expression / magnesium ion binding / protein homodimerization activity / extracellular exosome / cytosol
Similarity search - Function
Predicted HAD-superfamily phosphatase, subfamily IA/Epoxide hydrolase, N-terminal / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / alpha/beta hydrolase fold / haloacid dehalogenase-like hydrolase / Alpha/beta hydrolase fold-1 / HAD superfamily / HAD-like superfamily / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
: / PHOSPHATE ION / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, H. / Feng, Y. / Du, X.Y.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery of Phenylacylpiperidine as Novel sEH Inhibitors through Scaffold Hopping of Natural Stilbene.
Authors: Ding, J. / Zhu, M.Z. / Du, X.Y. / Liu, S.M. / Wang, H. / Liu, X.Z. / Xie, W.S. / Ma, H.L. / Feng, Y. / Zhu, X.H. / Liang, J.H.
History
DepositionNov 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3004
Polymers62,6861
Non-polymers6153
Water4,576254
1
A: Bifunctional epoxide hydrolase 2
hetero molecules

A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,6018
Polymers125,3712
Non-polymers1,2306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)91.507, 91.507, 242.802
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-821-

HOH

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Components

#1: Protein Bifunctional epoxide hydrolase 2


Mass: 62685.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHX2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P34913, soluble epoxide hydrolase, lipid-phosphate phosphatase
#2: Chemical ChemComp-A1EGG / 1-[1-[2-(3,5-dimethoxyphenyl)ethanoyl]piperidin-4-yl]-3-[[4-(trifluoromethyloxy)phenyl]methyl]urea


Mass: 495.491 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H28F3N3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→36.54 Å / Num. obs: 24318 / % possible obs: 99.44 % / Redundancy: 37.2 % / Biso Wilson estimate: 30.04 Å2 / CC1/2: 0.944 / Net I/σ(I): 13.55
Reflection shellResolution: 2.4→2.486 Å / Num. unique obs: 2336 / CC1/2: 0.751

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHENIX1.20.1_4487phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→36.54 Å / SU ML: 0.2322 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6525
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2381 2000 8.24 %
Rwork0.18 22284 -
obs0.1849 24284 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.27 Å2
Refinement stepCycle: LAST / Resolution: 2.4→36.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4339 0 41 254 4634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00574485
X-RAY DIFFRACTIONf_angle_d0.84076078
X-RAY DIFFRACTIONf_chiral_restr0.0457661
X-RAY DIFFRACTIONf_plane_restr0.0081789
X-RAY DIFFRACTIONf_dihedral_angle_d16.85781698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.26591370.18531524X-RAY DIFFRACTION99.11
2.46-2.530.24661390.18971548X-RAY DIFFRACTION99.29
2.53-2.60.26421390.17761551X-RAY DIFFRACTION99.41
2.6-2.680.27741410.19271559X-RAY DIFFRACTION99.36
2.68-2.780.25921380.20171556X-RAY DIFFRACTION99.24
2.78-2.890.29941400.19351557X-RAY DIFFRACTION99.3
2.89-3.020.24441410.17641563X-RAY DIFFRACTION99.65
3.02-3.180.27741400.18921572X-RAY DIFFRACTION99.65
3.18-3.380.23641430.18071594X-RAY DIFFRACTION99.48
3.38-3.640.20341430.16541588X-RAY DIFFRACTION99.83
3.64-4.010.19051440.16981596X-RAY DIFFRACTION99.49
4.01-4.590.21621460.15911639X-RAY DIFFRACTION99.78
4.59-5.780.2271490.18451652X-RAY DIFFRACTION99.72
5.78-36.540.25911600.19491785X-RAY DIFFRACTION99.79

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