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- PDB-6aum: Crystal structure of human soluble epoxide hydrolase complexed wi... -

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Basic information

Entry
Database: PDB / ID: 6aum
TitleCrystal structure of human soluble epoxide hydrolase complexed with trans-4-[4-(3-trifluoromethoxyphenyl-l-ureido)-cyclohexyloxy]-benzoic acid.
ComponentsBifunctional epoxide hydrolase 2
Keywordshydrolase/hydrolase inhibitor / soluble epoxide hydrolase / urea inhibitors / neuropathic pain / 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 / 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-BXV / PHOSPHATE ION / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsKodani, S.D. / Bahkta, S. / Hwang, S.H. / Pakhomova, S. / Newcomer, M.E. / Morisseau, C. / Hammock, B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01 ES002710 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)P42 ES004699 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL 107877 United States
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2018
Title: Identification and optimization of soluble epoxide hydrolase inhibitors with dual potency towards fatty acid amide hydrolase.
Authors: Kodani, S.D. / Bhakta, S. / Hwang, S.H. / Pakhomova, S. / Newcomer, M.E. / Morisseau, C. / Hammock, B.D.
History
DepositionSep 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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)63,3507
Polymers62,6861
Non-polymers6646
Water45025
1
A: Bifunctional epoxide hydrolase 2
hetero molecules

A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,69914
Polymers125,3712
Non-polymers1,32812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area5890 Å2
ΔGint-104 kcal/mol
Surface area42840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.713, 92.713, 243.736
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bifunctional epoxide hydrolase 2


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

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Non-polymers , 5 types, 31 molecules

#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-BXV / 4-{[trans-4-({[4-(trifluoromethoxy)phenyl]carbamoyl}amino)cyclohexyl]oxy}benzoic acid


Mass: 438.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21F3N2O5
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.41 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5 / Details: 30% PEG 3350, 0-10% sucrose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.38079 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 23, 2011 / Details: MIRRORS
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38079 Å / Relative weight: 1
ReflectionResolution: 2.95→40 Å / Num. obs: 13636 / % possible obs: 98.7 % / Redundancy: 2.8 % / Biso Wilson estimate: 78.9 Å2 / Rsym value: 0.11 / Net I/σ(I): 9.8
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1296 / Rsym value: 0.66 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S8O

1s8o


Resolution: 2.95→36.89 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.901 / SU B: 43.443 / SU ML: 0.363 / Cross valid method: THROUGHOUT / ESU R Free: 0.448 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2546 674 5 %RANDOM
Rwork0.19307 ---
obs0.19616 12929 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.387 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.23 Å2-0 Å2
2---0.45 Å20 Å2
3---1.47 Å2
Refinement stepCycle: 1 / Resolution: 2.95→36.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4331 0 40 25 4396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194493
X-RAY DIFFRACTIONr_bond_other_d0.0020.024199
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9776082
X-RAY DIFFRACTIONr_angle_other_deg0.94539763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.525550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06924.227194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.69815787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0971526
X-RAY DIFFRACTIONr_chiral_restr0.0710.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214916
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02901
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_it0.5252.8882194
X-RAY DIFFRACTIONr_mcbond_other0.5252.8872193
X-RAY DIFFRACTIONr_mcangle_it0.9254.3312743
X-RAY DIFFRACTIONr_mcangle_other0.9254.3312744
X-RAY DIFFRACTIONr_scbond_it0.5852.9742298
X-RAY DIFFRACTIONr_scbond_other0.5852.9762299
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8664.4383339
X-RAY DIFFRACTIONr_long_range_B_refined2.13233.694911
X-RAY DIFFRACTIONr_long_range_B_other2.13233.6944912
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.954→3.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 48 -
Rwork0.342 908 -
obs--97.85 %
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)
19.611-2.92571.31995.3484-0.92794.65240.2876-0.3047-0.7338-0.41310.17240.20950.3130.3727-0.460.2321-0.1340.07280.3035-0.09570.1773-20.2232-50.4183-10.8297
29.9595-1.6098-3.88770.64060.97882.07030.00950.5902-0.53280.0016-0.0433-0.12970.10930.09240.03380.3192-0.00730.01910.4455-0.05350.2459-15.9626-70.3328-5.4481
31.35631.0402-0.19740.8038-0.12332.0650.06080.0949-0.19840.05240.0934-0.1807-0.09820.3444-0.15420.2719-0.05550.03460.4075-0.11230.1857-17.8961-53.4429-2.5311
41.0121.319-0.47916.0137-1.82631.5441-0.2870.41080.2448-0.65260.51960.24320.1571-0.3329-0.23270.2845-0.15710.02890.4302-0.01150.1706-27.2533-49.5768-16.4239
50.90470.26060.11271.8238-0.5853.7428-0.0503-0.04410.0009-0.16880.15380.230.02810.0164-0.10350.1275-0.0218-0.00730.12910.02080.0318-23.5953-29.221113.4166
61.34640.078-0.02531.7304-0.65091.34020.0348-0.1270.11930.2205-0.0565-0.2513-0.31660.13810.02170.1412-0.0012-0.00830.16670.00880.0571-16.1076-20.620424.7345
71.5945-0.80690.6864.14740.42073.8351-0.12040.31070.3906-0.41170.06320.1215-0.43450.03910.05720.2064-0.0185-0.04170.19260.08930.1358-26.0339-8.885810.2907
82.12670.65590.81842.43570.6864.6713-0.08930.15870.0451-0.03420.0157-0.4946-0.03810.26350.07350.0752-0.02260.02290.15150.04130.1363-6.6174-20.635417.0871
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 24
2X-RAY DIFFRACTION2A25 - 75
3X-RAY DIFFRACTION3A76 - 152
4X-RAY DIFFRACTION4A153 - 222
5X-RAY DIFFRACTION5A223 - 283
6X-RAY DIFFRACTION6A284 - 382
7X-RAY DIFFRACTION7A383 - 468
8X-RAY DIFFRACTION8A469 - 548

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