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- PDB-3ant: Human soluble epoxide hydrolase in complex with a synthetic inhibitor -

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Basic information

Entry
Database: PDB / ID: 3ant
TitleHuman soluble epoxide hydrolase in complex with a synthetic inhibitor
ComponentsEpoxide hydrolase 2
KeywordsHydrolase/Hydrolase Inhibitor / hydrolase / Hydrolase-Hydrolase Inhibitor 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 / epoxide metabolic process / Biosynthesis of maresins / soluble epoxide hydrolase / 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 / epoxide metabolic process / Biosynthesis of maresins / soluble epoxide hydrolase / lysophosphatidic acid phosphatase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / epoxide hydrolase activity / regulation of cholesterol metabolic process / phosphatase activity / peroxisomal matrix / toxic substance binding / dephosphorylation / cholesterol homeostasis / 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 / haloacid dehalogenase-like hydrolase / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / HAD superfamily / HAD-like superfamily / Alpha/Beta hydrolase fold, catalytic domain ...Predicted HAD-superfamily phosphatase, subfamily IA/Epoxide hydrolase, N-terminal / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / haloacid dehalogenase-like hydrolase / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / HAD superfamily / HAD-like superfamily / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-S82 / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChiyo, N. / Ishii, T. / Hourai, S. / Yanagi, K.
CitationJournal: J.Med.Chem. / Year: 2011
Title: A practical use of ligand efficiency indices out of the fragment-based approach: ligand efficiency-guided lead identification of soluble epoxide hydrolase inhibitors
Authors: Tanaka, D. / Tsuda, Y. / Shiyama, T. / Nishimura, T. / Chiyo, N. / Tominaga, Y. / Sawada, N. / Mimoto, T. / Kusunose, N.
History
DepositionSep 8, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Feb 24, 2021Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_ref_seq_dif / struct_site
Item: _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id ..._struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epoxide hydrolase 2
B: Epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0024
Polymers77,2932
Non-polymers7092
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.384, 80.296, 88.867
Angle α, β, γ (deg.)90.000, 125.880, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Epoxide hydrolase 2 / / Soluble epoxide hydrolase / SEH / Epoxide hydratase / Cytosolic epoxide hydrolase / CEH


Mass: 38646.422 Da / Num. of mol.: 2 / Fragment: hydrolase domain, UNP residues 230-555
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHX2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P34913, soluble epoxide hydrolase
#2: Chemical ChemComp-S82 / 4-[3-(1-methylethyl)-1,2,4-oxadiazol-5-yl]-N-[(1S,2R)-2-phenylcyclopropyl]piperidine-1-carboxamide


Mass: 354.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.16 % / Mosaicity: 0.819 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 20%(w/v) PEG 8000, 200mM sodium iodide, pH 7.3, vapor diffusion, sitting drop, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 28466 / % possible obs: 99.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.059 / Χ2: 1.96 / Net I/σ(I): 16.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.443.40.17913721.403194.9
2.44-2.493.50.17713281.436196.3
2.49-2.533.60.17514251.379197.5
2.53-2.593.70.14913861.529198.3
2.59-2.643.70.14814151.374199.1
2.64-2.73.80.13214481.478199.9
2.7-2.773.80.12514221.5281100
2.77-2.853.80.11314221.6391100
2.85-2.933.80.114251.5931100
2.93-3.023.80.08914211.7881100
3.02-3.133.80.07414211.751100
3.13-3.263.80.07114262.0611100
3.26-3.413.80.06714652.2971100
3.41-3.583.80.06114222.6121100
3.58-3.813.80.05814402.924199.9
3.81-4.13.80.05314262.8531100
4.1-4.523.80.04514372.7111100
4.52-5.173.80.04114572.281100
5.17-6.513.80.03914472.138199.9
6.51-503.60.03314612.164197.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ANS

3ans


Resolution: 2.4→35.07 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.2311 / WRfactor Rwork: 0.2005 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8343 / SU B: 7.61 / SU ML: 0.18 / SU R Cruickshank DPI: 0.4564 / SU Rfree: 0.2571 / Cross valid method: THROUGHOUT / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 1439 5.1 %RANDOM
Rwork0.1994 ---
obs0.2014 28433 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 82.53 Å2 / Biso mean: 36.4799 Å2 / Biso min: 13.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.04 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→35.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5066 0 52 121 5239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225276
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.967160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6035626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81923.934244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33515880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9051528
X-RAY DIFFRACTIONr_chiral_restr0.0830.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214100
X-RAY DIFFRACTIONr_mcbond_it0.6041.53142
X-RAY DIFFRACTIONr_mcangle_it1.16425078
X-RAY DIFFRACTIONr_scbond_it1.52232134
X-RAY DIFFRACTIONr_scangle_it2.5944.52076
LS refinement shellResolution: 2.404→2.466 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 108 -
Rwork0.243 1792 -
all-1900 -
obs--90 %

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