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- PDB-4jnc: Soluble Epoxide Hydrolase complexed with a carboxamide inhibitor -

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Basic information

Entry
Database: PDB / ID: 4jnc
TitleSoluble Epoxide Hydrolase complexed with a carboxamide inhibitor
ComponentsBifunctional epoxide hydrolase 2
KeywordsHydrolase/hydrolase inhibitor / epoxide 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-1LF / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsShewchuk, L.M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Discovery of 1-(1,3,5-triazin-2-yl)piperidine-4-carboxamides as inhibitors of soluble epoxide hydrolase.
Authors: Thalji, R.K. / McAtee, J.J. / Belyanskaya, S. / Brandt, M. / Brown, G.D. / Costell, M.H. / Ding, Y. / Dodson, J.W. / Eisennagel, S.H. / Fries, R.E. / Gross, J.W. / Harpel, M.R. / Holt, D.A. ...Authors: Thalji, R.K. / McAtee, J.J. / Belyanskaya, S. / Brandt, M. / Brown, G.D. / Costell, M.H. / Ding, Y. / Dodson, J.W. / Eisennagel, S.H. / Fries, R.E. / Gross, J.W. / Harpel, M.R. / Holt, D.A. / Israel, D.I. / Jolivette, L.J. / Krosky, D. / Li, H. / Lu, Q. / Mandichak, T. / Roethke, T. / Schnackenberg, C.G. / Schwartz, B. / Shewchuk, L.M. / Xie, W. / Behm, D.J. / Douglas, S.A. / Shaw, A.L. / Marino, J.P.
History
DepositionMar 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 20, 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: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5442
Polymers36,1351
Non-polymers4081
Water4,288238
1
A: Bifunctional epoxide hydrolase 2
hetero molecules

A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0884
Polymers72,2712
Non-polymers8172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)80.285, 91.951, 45.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 36135.410 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHX2 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P34913, soluble epoxide hydrolase, lipid-phosphate phosphatase
#2: Chemical ChemComp-1LF / 1-[4-methyl-6-(methylamino)-1,3,5-triazin-2-yl]-N-[2-(trifluoromethyl)benzyl]piperidine-4-carboxamide


Mass: 408.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23F3N6O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG3350, 0.1 M BisTris, 0.2M NH4OAc, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 18, 2007 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.96→60.48 Å / Num. all: 23361 / Num. obs: 23361 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 33
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 6.5 / Num. unique all: 1493 / % possible all: 86.66

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VJ5

1vj5


Resolution: 1.96→60.48 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.002 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.179 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 1254 5.1 %RANDOM
Rwork0.18678 ---
obs0.1884 23361 98.51 %-
all-23361 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.936 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.96→60.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 29 238 2745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222635
X-RAY DIFFRACTIONr_angle_refined_deg0.971.9633595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1815329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79724.017117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85115432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4611512
X-RAY DIFFRACTIONr_chiral_restr0.0660.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212033
X-RAY DIFFRACTIONr_mcbond_it0.2821.51586
X-RAY DIFFRACTIONr_mcangle_it0.5422561
X-RAY DIFFRACTIONr_scbond_it0.77431049
X-RAY DIFFRACTIONr_scangle_it1.3114.51025
LS refinement shellResolution: 1.96→2.014 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 85 -
Rwork0.304 1493 -
obs-1493 86.66 %
Refinement TLS params.Method: refined / Origin x: -10.306 Å / Origin y: 19.032 Å / Origin z: -15.356 Å
111213212223313233
T0.0222 Å20.0088 Å2-0.0056 Å2-0.036 Å2-0.0022 Å2--0.0537 Å2
L0.8682 °20.0061 °2-0.0822 °2-0.6488 °20.0561 °2--1.0977 °2
S-0.0099 Å °-0.021 Å °0.062 Å °0.0229 Å °0.0046 Å °0.0304 Å °-0.1157 Å °-0.028 Å °0.0053 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A237 - 548
2X-RAY DIFFRACTION1A701 - 938

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