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- PDB-5k0i: mpges1 bound to an inhibitor -

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Basic information

Entry
Database: PDB / ID: 5k0i
Titlempges1 bound to an inhibitor
ComponentsProstaglandin E synthase
KeywordsIsomerase/Isomerase Inhibitor / mpges1 / inhibitor / pain / inflammation / Isomerase-Isomerase Inhibitor complex
Function / homology
Function and homology information


prostaglandin-E synthase / prostaglandin-E synthase activity / regulation of fever generation / prostaglandin-D synthase activity / glutathione binding / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / positive regulation of prostaglandin secretion / glutathione peroxidase activity / prostaglandin biosynthetic process / prostaglandin metabolic process ...prostaglandin-E synthase / prostaglandin-E synthase activity / regulation of fever generation / prostaglandin-D synthase activity / glutathione binding / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / positive regulation of prostaglandin secretion / glutathione peroxidase activity / prostaglandin biosynthetic process / prostaglandin metabolic process / nuclear envelope lumen / glutathione transferase / glutathione transferase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / sensory perception of pain / regulation of inflammatory response / cell population proliferation / negative regulation of cell population proliferation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / signal transduction / membrane
Similarity search - Function
Microsomal glutathione S-transferase 1-like / Membrane associated eicosanoid/glutathione metabolism-like domain / Membrane-associated, eicosanoid/glutathione metabolism (MAPEG) protein / Membrane associated eicosanoid/glutathione metabolism-like domain superfamily / MAPEG family / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6PW / GLUTATHIONE / Prostaglandin E synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.3 Å
AuthorsLuz, J.G. / Kuklish, S.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2016
Title: Characterization of 3,3-dimethyl substituted N-aryl piperidines as potent microsomal prostaglandin E synthase-1 inhibitors.
Authors: Kuklish, S.L. / Antonysamy, S. / Bhattachar, S.N. / Chandrasekhar, S. / Fisher, M.J. / Fretland, A.J. / Gooding, K. / Harvey, A. / Hughes, N.E. / Luz, J.G. / Manninen, P.R. / McGee, J.E. / ...Authors: Kuklish, S.L. / Antonysamy, S. / Bhattachar, S.N. / Chandrasekhar, S. / Fisher, M.J. / Fretland, A.J. / Gooding, K. / Harvey, A. / Hughes, N.E. / Luz, J.G. / Manninen, P.R. / McGee, J.E. / Navarro, A. / Norman, B.H. / Partridge, K.M. / Quimby, S.J. / Schiffler, M.A. / Sloan, A.V. / Warshawsky, A.M. / York, J.S. / Yu, X.P.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prostaglandin E synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0167
Polymers17,3241
Non-polymers1,6926
Water2,396133
1
A: Prostaglandin E synthase
hetero molecules

A: Prostaglandin E synthase
hetero molecules

A: Prostaglandin E synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,04721
Polymers51,9713
Non-polymers5,07618
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area14900 Å2
ΔGint-51 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.444, 77.444, 123.565
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-375-

HOH

21A-421-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein Prostaglandin E synthase / Microsomal glutathione S-transferase 1-like 1 / MGST1-L1 / Microsomal prostaglandin E synthase 1 / ...Microsomal glutathione S-transferase 1-like 1 / MGST1-L1 / Microsomal prostaglandin E synthase 1 / MPGES-1 / p53-induced gene 12 protein


Mass: 17323.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTGES, MGST1L1, MPGES1, PGES, PIG12 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O14684, prostaglandin-E synthase
#4: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 137 molecules

#2: Chemical ChemComp-6PW / 1,5-anhydro-2,3,4-trideoxy-3-{[(4S)-3,3-dimethyl-1-(8-methylquinolin-2-yl)piperidine-4-carbonyl]amino}-D-erythro-hexitol


Mass: 411.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H33N3O3
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 4.12 Å3/Da / Density % sol: 70.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M tris pH 9.4, 36% PEG 1K

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.26→19.65 Å / Num. obs: 74628 / % possible obs: 99.9 % / Redundancy: 5.6 % / Net I/σ(I): 6.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.3→19.65 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.963 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.15917 3447 5.1 %RANDOM
Rwork0.14549 ---
obs0.14619 64481 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.208 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.3→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 110 133 1415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211400
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.04221907
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.4575.06167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91320.9851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89515212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7131511
X-RAY DIFFRACTIONr_chiral_restr0.0610.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211016
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.9333792
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.17251293
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.2988608
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.24911609
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.01531400
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 239 -
Rwork0.301 4769 -
obs--100 %

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