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- PDB-8s75: Soluble epoxide hydrolase in complex with PROTAC FL412 -

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Basic information

Entry
Database: PDB / ID: 8s75
TitleSoluble epoxide hydrolase in complex with PROTAC FL412
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 / soluble epoxide hydrolase / epoxide metabolic process / lysophosphatidic acid phosphatase activity / 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 / soluble epoxide hydrolase / epoxide metabolic process / lysophosphatidic acid phosphatase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / epoxide hydrolase activity / regulation of cholesterol metabolic process / dephosphorylation / phosphatase activity / peroxisomal matrix / toxic substance binding / cholesterol homeostasis / regulation of cell growth / Peroxisomal protein import / 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
: / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsKumar, A. / Schoenfeld, J. / Hiesinger, K. / Lillich, F. / Proschak, E. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)530858826 Germany
Fraunhofer Cluster of Excellence Immune-Mediated Diseases Germany
CitationJournal: To Be Published
Title: Soluble epoxide hydrolase in complex with PROTAC FL412
Authors: Kumar, A. / Schoenfeld, J. / Hiesinger, K. / Lillich, F. / Proschak, E. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionFeb 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: 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
B: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,47312
Polymers83,9022
Non-polymers2,57110
Water8,593477
1
A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4899
Polymers41,9511
Non-polymers1,5388
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9843
Polymers41,9511
Non-polymers1,0332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.125, 80.182, 89.417
Angle α, β, γ (deg.)90.00, 91.54, 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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-A1H5L / ~{N}-[2-[2-[2-[2-[2-[2-[2-[2,6-bis(oxidanylidene)piperidin-3-yl]-1,3-bis(oxidanylidene)isoindol-4-yl]oxyethanoylamino]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]-4-[4-[[4-(trifluoromethyloxy)phenyl]carbamoylamino]cyclohexyl]oxy-benzamide


Mass: 970.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C46H53F3N6O14 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.01 Å3/Da / Density % sol: 38.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 20% w/v PEG 3350, 0.2M Ammonium 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: 1.42→47.15 Å / Num. obs: 124511 / % possible obs: 99.3 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.046 / Rrim(I) all: 0.085 / Χ2: 0.95 / Net I/σ(I): 9.4
Reflection shellResolution: 1.42→1.44 Å / % possible obs: 97.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.989 / Num. measured all: 21097 / Num. unique obs: 6064 / CC1/2: 0.592 / Rpim(I) all: 0.63 / Rrim(I) all: 1.177 / Χ2: 0.94 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→47.15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.493 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21972 6472 5.2 %RANDOM
Rwork0.18733 ---
obs0.18904 118003 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.737 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å2-0.55 Å2
2---1.28 Å2-0 Å2
3---0.66 Å2
Refinement stepCycle: 1 / Resolution: 1.42→47.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5088 0 103 477 5668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0125452
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164985
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.837415
X-RAY DIFFRACTIONr_angle_other_deg0.6221.7411512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1085668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.1558.33345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53910872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.2769
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026482
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021283
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_it2.1312.2712630
X-RAY DIFFRACTIONr_mcbond_other2.1272.272630
X-RAY DIFFRACTIONr_mcangle_it3.0944.0883309
X-RAY DIFFRACTIONr_mcangle_other3.0944.0893310
X-RAY DIFFRACTIONr_scbond_it2.7552.4742822
X-RAY DIFFRACTIONr_scbond_other2.7552.4742823
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2074.4394106
X-RAY DIFFRACTIONr_long_range_B_refined6.00722.866342
X-RAY DIFFRACTIONr_long_range_B_other6.00722.866343
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.42→1.456 Å
RfactorNum. reflection% reflection
Rfree0.335 467 -
Rwork0.321 8667 -
obs--98.37 %

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