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- PDB-8qzd: Soluble epoxide hydrolase in complex with Epoxykinin -

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Basic information

Entry
Database: PDB / ID: 8qzd
TitleSoluble epoxide hydrolase in complex with Epoxykinin
ComponentsBifunctional epoxide hydrolase 2
KeywordsHYDROLASE / COMPLEX / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
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
BROMIDE ION / : / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKumar, A. / Ehrler, J.M.H. / Ziegler, S. / Doetsch, L. / Proschak, E. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding supportEuropean Union, Switzerland, 3items
OrganizationGrant numberCountry
European Union (EU)EFRE-0200481European Union
Innovative Medicines Initiative115489 Switzerland
European Communitys Seventh Framework ProgrammeFP7/2007-2013European Union
CitationJournal: J.Med.Chem. / Year: 2024
Title: Discovery of the sEH Inhibitor Epoxykynin as a Potent Kynurenine Pathway Modulator.
Authors: Dotsch, L. / Davies, C. / Hennes, E. / Schonfeld, J. / Kumar, A. / Guita, C.D.C.L. / Ehrler, J.H.M. / Hiesinger, K. / Thavam, S. / Janning, P. / Sievers, S. / Knapp, S. / Proschak, E. / ...Authors: Dotsch, L. / Davies, C. / Hennes, E. / Schonfeld, J. / Kumar, A. / Guita, C.D.C.L. / Ehrler, J.H.M. / Hiesinger, K. / Thavam, S. / Janning, P. / Sievers, S. / Knapp, S. / Proschak, E. / Ziegler, S. / Waldmann, H.
History
DepositionOct 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,22115
Polymers41,9511
Non-polymers1,27014
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint33 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.924, 80.312, 89.084
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Bifunctional epoxide hydrolase 2


Mass: 41951.086 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 (E. coli)
References: UniProt: P34913, soluble epoxide hydrolase, lipid-phosphate phosphatase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-XDZ / 2-[5-bromanyl-3-[2,2,2-tris(fluoranyl)ethanoyl]indol-1-yl]-N-cycloheptyl-ethanamide / Epoxykinin


Mass: 445.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20BrF3N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 1.96 Å3/Da / Density % sol: 37.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% PEG Smear High, 0.1M PIPES pH 7.0, 0.1M magnesium formate, 0.1M rubidium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→44.54 Å / Num. obs: 80739 / % possible obs: 99.6 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.032 / Rrim(I) all: 0.082 / Χ2: 0.9 / Net I/σ(I): 10.7 / Num. measured all: 518234
Reflection shellResolution: 1.3→1.33 Å / % possible obs: 93.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 1.149 / Num. measured all: 21137 / Num. unique obs: 3673 / CC1/2: 0.573 / Rpim(I) all: 0.517 / Rrim(I) all: 1.263 / Χ2: 0.75 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→44.54 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.8 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18041 4091 5.1 %RANDOM
Rwork0.16279 ---
obs0.16371 76583 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-0 Å2-0 Å2
2---0.82 Å20 Å2
3---0.6 Å2
Refinement stepCycle: 1 / Resolution: 1.3→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2553 0 76 258 2887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122837
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162610
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.8343853
X-RAY DIFFRACTIONr_angle_other_deg0.6551.7396039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8715350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.1996.66718
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16510462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023386
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02660
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6241.7781358
X-RAY DIFFRACTIONr_mcbond_other1.6031.7771358
X-RAY DIFFRACTIONr_mcangle_it2.3733.1831722
X-RAY DIFFRACTIONr_mcangle_other2.3783.1851723
X-RAY DIFFRACTIONr_scbond_it2.7332.0521479
X-RAY DIFFRACTIONr_scbond_other2.7322.0531480
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9753.6372132
X-RAY DIFFRACTIONr_long_range_B_refined5.26220.133338
X-RAY DIFFRACTIONr_long_range_B_other5.26220.123338
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.304→1.338 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 295 -
Rwork0.287 5354 -
obs--95.91 %

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