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- PDB-8s77: Soluble epoxide hydrolase in complex with PROTAC JSF234 -

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Basic information

Entry
Database: PDB / ID: 8s77
TitleSoluble epoxide hydrolase in complex with PROTAC JSF234
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 / Peroxisomal protein import / cholesterol homeostasis / 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
: / DI(HYDROXYETHYL)ETHER / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsKumar, A. / Schoenfeld, J. / Hiesinger, K. / Lillich, F. / Proschak, E. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)530858826 Germany
CitationJournal: J.Med.Chem. / Year: 2025
Title: Structure-Based Design of PROTACS for the Degradation of Soluble Epoxide Hydrolase.
Authors: Schonfeld, J. / Brunst, S. / Ciomirtan, L. / Willmer, L. / Chromik, M.A. / Kumar, A. / Froemel, T. / Liebisch, N. / Hackspacher, A. / Ehrler, J.H.M. / Wintermeier, L. / Hesse, C. / Fiedler, ...Authors: Schonfeld, J. / Brunst, S. / Ciomirtan, L. / Willmer, L. / Chromik, M.A. / Kumar, A. / Froemel, T. / Liebisch, N. / Hackspacher, A. / Ehrler, J.H.M. / Wintermeier, L. / Hesse, C. / Fiedler, J. / Heering, J. / Freitag, H. / Zardo, P. / Fieguth, H.G. / Bruggerhoff, A. / Jakob, J. / Haupl, B. / Weizel, L. / Kaiser, A. / Schubert-Zsilavecz, M. / Oellerich, T. / Fleming, I. / Schebb, N.H. / Furst, R. / Kannt, A. / Knapp, S. / Proschak, E. / Hiesinger, K.
History
DepositionFeb 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 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

Downloads & links

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Assembly

Deposited unit
A: Bifunctional epoxide hydrolase 2
B: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,50212
Polymers83,9022
Non-polymers1,60010
Water6,575365
1
A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8538
Polymers41,9511
Non-polymers9027
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6494
Polymers41,9511
Non-polymers6983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.283, 80.337, 89.248
Angle α, β, γ (deg.)90.00, 91.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bifunctional epoxide hydrolase 2


Mass: 41951.086 Da / Num. of mol.: 2
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.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-A1H5J / ~{N}-[[4-(cyclopropylsulfonylamino)-2-(trifluoromethyl)phenyl]methyl]-1-ethylsulfonyl-indole-5-carboxamide


Mass: 529.552 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H22F3N3O5S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG6000, 10% ethylene glycol, 0.1M tris pH 7.5, 0.1M magnesium 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: 1.36→47.3 Å / Num. obs: 141572 / % possible obs: 98.8 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.028 / Rrim(I) all: 0.051 / Χ2: 0.94 / Net I/σ(I): 11.7
Reflection shellResolution: 1.36→1.38 Å / % possible obs: 98.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 1.062 / Num. measured all: 22251 / Num. unique obs: 6994 / CC1/2: 0.574 / Rpim(I) all: 0.706 / Rrim(I) all: 1.281 / Χ2: 0.87 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→47.3 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.45 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21493 6949 4.9 %RANDOM
Rwork0.19429 ---
obs0.19531 134595 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.476 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0 Å2-0.82 Å2
2---1.51 Å2-0 Å2
3---0.96 Å2
Refinement stepCycle: 1 / Resolution: 1.36→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5045 0 105 365 5515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0125534
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165011
X-RAY DIFFRACTIONr_angle_refined_deg1.8381.8297558
X-RAY DIFFRACTIONr_angle_other_deg0.6221.74211553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.7617.19541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01610871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.2781
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026679
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021319
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_it2.52.7512694
X-RAY DIFFRACTIONr_mcbond_other2.52.7512694
X-RAY DIFFRACTIONr_mcangle_it3.6754.9483406
X-RAY DIFFRACTIONr_mcangle_other3.6754.9513407
X-RAY DIFFRACTIONr_scbond_it2.9482.8632840
X-RAY DIFFRACTIONr_scbond_other2.9482.8632841
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4565.1964147
X-RAY DIFFRACTIONr_long_range_B_refined6.25327.236433
X-RAY DIFFRACTIONr_long_range_B_other6.22426.696352
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.36→1.394 Å
RfactorNum. reflection% reflection
Rfree0.344 517 -
Rwork0.351 9973 -
obs--99.11 %

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