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- PDB-3otq: Soluble Epoxide Hydrolase in complex with pyrazole antagonist -

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Basic information

Entry
Database: PDB / ID: 3otq
TitleSoluble Epoxide Hydrolase in complex with pyrazole antagonist
ComponentsEpoxide hydrolase 2
KeywordsHYDROLASE / epoxide hydrolase
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 / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / haloacid dehalogenase-like hydrolase / alpha/beta hydrolase fold / HAD superfamily/HAD-like / Alpha/beta hydrolase fold-1 / HAD superfamily ...Predicted HAD-superfamily phosphatase, subfamily IA/Epoxide hydrolase, N-terminal / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / haloacid dehalogenase-like hydrolase / alpha/beta hydrolase fold / HAD superfamily/HAD-like / Alpha/beta hydrolase fold-1 / HAD superfamily / HAD-like superfamily / Alpha/Beta hydrolase fold, catalytic domain / DNA polymerase; domain 1 / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-MZL / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFarrow, N.A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: Substituted pyrazoles as novel sEH antagonist: investigation of key binding interactions within the catalytic domain.
Authors: Lo, H.Y. / Man, C.C. / Fleck, R.W. / Farrow, N.A. / Ingraham, R.H. / Kukulka, A. / Proudfoot, J.R. / Betageri, R. / Kirrane, T. / Patel, U. / Sharma, R. / Hoermann, M.A. / Kabcenell, A. / Lombaert, S.D.
History
DepositionSep 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 24, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_site
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0552
Polymers62,6861
Non-polymers3691
Water73941
1
A: Epoxide hydrolase 2
hetero molecules

A: Epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,1104
Polymers125,3712
Non-polymers7392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area4270 Å2
ΔGint-8 kcal/mol
Surface area43560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.993, 92.993, 243.651
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

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Components

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


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 (E. coli) / References: UniProt: P34913, soluble epoxide hydrolase
#2: Chemical ChemComp-MZL / N-[4-(5-ethyl-3-pyridin-3-yl-1H-pyrazol-1-yl)phenyl]pyridine-3-carboxamide


Mass: 369.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H19N5O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.29 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 12861

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Processing

Software
NameClassification
CrystalCleardata collection
CNXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å
RfactorNum. reflection
Rfree0.3183 655
Rwork0.2301 -
obs-12861
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4316 0 28 41 4385

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