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- PDB-8zbl: Glycosidated glycyrrhetinic acid derivative as a soluble epoxide ... -

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Basic information

Entry
Database: PDB / ID: 8zbl
TitleGlycosidated glycyrrhetinic acid derivative as a soluble epoxide hydrolase inhibitor
ComponentsBifunctional epoxide hydrolase 2
KeywordsHYDROLASE / 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: 2.7 Å
AuthorsWang, H. / Feng, Y. / Ge, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Eur.J.Med.Chem. / Year: 2024
Title: Discovery of glycosidated glycyrrhetinic acid derivatives: Natural product-based soluble epoxide hydrolase inhibitors.
Authors: Liu, Q. / Wang, Y.X. / Ge, Z.H. / Zhu, M.Z. / Ding, J. / Wang, H. / Liu, S.M. / Liu, R.C. / Li, C. / Yu, M.J. / Feng, Y. / Zhu, X.H. / Liang, J.H.
History
DepositionApr 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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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)63,5644
Polymers62,6861
Non-polymers8783
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-7 kcal/mol
Surface area23990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.093, 93.093, 245.365
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

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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-A1D78 / 1-[[(2~{S},4~{a}~{S},6~{a}~{R},6~{a}~{S},6~{b}~{R},8~{a}~{R},10~{S},12~{a}~{S},14~{b}~{S})-10-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2,4~{a},6~{a},6~{b},9,9,12~{a}-heptamethyl-13-oxidanylidene-3,4,5,6,6~{a},7,8,8~{a},10,11,12,14~{b}-dodecahydro-1~{H}-picen-2-yl]methyl]-3-(oxan-4-ylmethyl)urea


Mass: 759.024 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H70N2O9 / 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
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS pH 6.5; 28% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→57.42 Å / Num. obs: 18116 / % possible obs: 99.26 % / Redundancy: 35.6 % / Biso Wilson estimate: 37.67 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.59
Reflection shellResolution: 2.7→2.797 Å / Num. unique obs: 1764 / CC1/2: 0.964

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PHENIXphasing
Cootmodel building
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→57.42 Å / SU ML: 0.2634 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.0922
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2639 932 5.18 %
Rwork0.2093 17066 -
obs0.212 17998 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.38 Å2
Refinement stepCycle: LAST / Resolution: 2.7→57.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4323 0 60 128 4511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00554491
X-RAY DIFFRACTIONf_angle_d0.85326101
X-RAY DIFFRACTIONf_chiral_restr0.0529673
X-RAY DIFFRACTIONf_plane_restr0.0073776
X-RAY DIFFRACTIONf_dihedral_angle_d16.58431706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.840.27861240.24012383X-RAY DIFFRACTION99.92
2.84-3.020.36811330.27052385X-RAY DIFFRACTION99.8
3.02-3.250.32351210.23472387X-RAY DIFFRACTION99.64
3.25-3.580.27481420.232415X-RAY DIFFRACTION99.38
3.58-4.10.2411510.19232370X-RAY DIFFRACTION98.28
4.1-5.160.21481230.17522472X-RAY DIFFRACTION99.01
5.16-57.420.2571380.19992654X-RAY DIFFRACTION99.43

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