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- PDB-4hai: Crystal structure of human soluble epoxide hydrolase complexed wi... -

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Basic information

Entry
Database: PDB / ID: 4hai
TitleCrystal structure of human soluble epoxide hydrolase complexed with N-cycloheptyl-1-(mesitylsulfonyl)piperidine-4-carboxamide.
ComponentsBifunctional epoxide hydrolase 2
Keywordshydrolase/hydrolase inhibitor / DOMAIN-SWAPPED DIMER / 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 / 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 / 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 / HAD superfamily/HAD-like / alpha/beta hydrolase fold / haloacid dehalogenase-like hydrolase / 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 / HAD superfamily/HAD-like / alpha/beta hydrolase fold / haloacid dehalogenase-like hydrolase / 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-I23 / PHOSPHATE ION / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsPecic, S. / Pakhomova, S. / Newcomer, M.E. / Morisseau, C. / Hammock, B.D. / Zhu, Z. / Deng, S.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Synthesis and structure-activity relationship of piperidine-derived non-urea soluble epoxide hydrolase inhibitors.
Authors: Pecic, S. / Pakhomova, S. / Newcomer, M.E. / Morisseau, C. / Hammock, B.D. / Zhu, Z. / Rinderspacher, A. / Deng, S.X.
History
DepositionSep 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)63,2114
Polymers62,6861
Non-polymers5263
Water48627
1
A: Bifunctional epoxide hydrolase 2
hetero molecules

A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4238
Polymers125,3712
Non-polymers1,0526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area4920 Å2
ΔGint-49 kcal/mol
Surface area43220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.320, 92.320, 243.982
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Bifunctional epoxide hydrolase 2 / Cytosolic epoxide hydrolase 2 / CEH / Epoxide hydratase / Soluble epoxide hydrolase / SEH / Lipid- ...Cytosolic epoxide hydrolase 2 / CEH / Epoxide hydratase / Soluble epoxide hydrolase / SEH / Lipid-phosphate phosphatase


Mass: 62685.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHX2 / Plasmid: ACHSEH1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P34913, soluble epoxide hydrolase, lipid-phosphate phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-I23 / N-cycloheptyl-1-[(2,4,6-trimethylphenyl)sulfonyl]piperidine-4-carboxamide


Mass: 406.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H34N2O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 3350, 0-10% sucrose , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.55→79.95 Å / Num. all: 20842 / Num. obs: 20842 / % possible obs: 99.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 68.8 Å2 / Rsym value: 0.07 / Net I/σ(I): 18
Reflection shellResolution: 2.55→2.68 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 2439 / Rsym value: 0.7 / % possible all: 95.9

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Processing

Software
NameVersionClassification
xia2data scaling
MOLREPphasing
REFMAC5.6.0117refinement
xia2data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S8O

1s8o


Resolution: 2.55→79.95 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 22.694 / SU ML: 0.226 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.662 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 1068 5.1 %RANDOM
Rwork0.18005 ---
all0.18281 19762 --
obs0.18281 19762 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.849 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20.8 Å20 Å2
2--1.6 Å20 Å2
3----2.4 Å2
Refinement stepCycle: LAST / Resolution: 2.55→79.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4328 0 34 27 4389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.024472
X-RAY DIFFRACTIONr_bond_other_d0.0010.023090
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9796056
X-RAY DIFFRACTIONr_angle_other_deg0.8837548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2255547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15924.219192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95115780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5411526
X-RAY DIFFRACTIONr_chiral_restr0.0730.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214895
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02888
LS refinement shellResolution: 2.546→2.612 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 65 -
Rwork0.307 1142 -
obs-1142 90.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.5365-5.3762-3.61544.55643.61873.37310.2781-0.12940.2929-0.66490.0049-0.234-0.6691-0.1647-0.2830.4033-0.0853-0.04320.18720.06850.081420.337749.6809-11.3357
25.8533-1.28172.6631.3983-1.59772.2374-0.25060.49890.40290.20550.0141-0.189-0.14550.01130.23640.184-0.0633-0.06820.18520.05330.048415.685170.0946-5.6048
30.53020.42860.55261.4340.63380.6406-0.16440.0467-0.0085-0.18580.1979-0.0214-0.13230.022-0.03350.1137-0.0881-0.01520.1580.04970.038121.870951.2296-8.896
40.21460.22380.02051.2320.03110.48320.02850.0021-0.04320.0237-0.0290.0344-0.05450.01830.00050.0754-0.0076-0.01430.0909-0.01910.080419.767825.662320.9651
50.8636-0.0236-0.27091.2629-0.09641.02-0.03610.0981-0.1849-0.14810.00280.07780.1725-0.06780.03330.08-0.023-0.01070.0583-0.05090.071915.885713.564214.4605
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 23
2X-RAY DIFFRACTION2A24 - 75
3X-RAY DIFFRACTION3A76 - 225
4X-RAY DIFFRACTION4A226 - 368
5X-RAY DIFFRACTION5A369 - 548

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