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- PDB-2xyw: Novel Sulfonylthiadiazoles with an Unusual Binding Mode as Partia... -

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Basic information

Entry
Database: PDB / ID: 2xyw
TitleNovel Sulfonylthiadiazoles with an Unusual Binding Mode as Partial Dual Peroxisome Proliferator-Activated Receptor (PPAR) gamma-delta Agonists with High Potency and In-vivo Efficacy
ComponentsPEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA
KeywordsTRANSCRIPTION / DNA-BINDING / TRANSCRIPTION REGULATION / RECEPTOR / ACTIVATOR / ZINC-FINGER
Function / homology
Function and homology information


fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / positive regulation of epidermis development / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / D-glucose transmembrane transport / negative regulation of smooth muscle cell migration ...fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / positive regulation of epidermis development / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / D-glucose transmembrane transport / negative regulation of smooth muscle cell migration / positive regulation of myoblast proliferation / proteoglycan metabolic process / fatty acid catabolic process / negative regulation of collagen biosynthetic process / positive regulation of fatty acid oxidation / phospholipid biosynthetic process / Carnitine shuttle / negative regulation of myoblast differentiation / response to vitamin A / Signaling by Retinoic Acid / positive regulation of fatty acid metabolic process / nuclear steroid receptor activity / fatty acid beta-oxidation / negative regulation of cholesterol storage / cell-substrate adhesion / positive regulation of insulin secretion involved in cellular response to glucose stimulus / decidualization / keratinocyte proliferation / positive regulation of fat cell differentiation / adipose tissue development / NF-kappaB binding / cellular response to nutrient levels / fatty acid transport / response to glucose / energy homeostasis / intracellular receptor signaling pathway / hormone-mediated signaling pathway / embryo implantation / cholesterol metabolic process / negative regulation of miRNA transcription / response to activity / fatty acid metabolic process / generation of precursor metabolites and energy / phosphatidylinositol 3-kinase/protein kinase B signal transduction / apoptotic signaling pathway / negative regulation of smooth muscle cell proliferation / wound healing / transcription coactivator binding / negative regulation of cell growth / Nuclear Receptor transcription pathway / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / nuclear receptor activity / glucose metabolic process / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / vasodilation / heart development / cellular response to lipopolysaccharide / cellular response to hypoxia / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / apoptotic process / lipid binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Peroxisome proliferator-activated receptor, beta / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. ...Peroxisome proliferator-activated receptor, beta / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-08S / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsMarquette, J.-P. / Mathieu, M.
CitationJournal: Chemmedchem / Year: 2011
Title: Sulfonylthiadiazoles with an Unusual Binding Mode as Partial Dual Peroxisome Proliferator-Activated Receptor (Ppar) Gamma / Delta Agonists with High Potency and in-Vivo Efficacy
Authors: Keil, S. / Matter, H. / Schonafinger, K. / Glien, M. / Mathieu, M. / Marquette, J.-P. / Michot, N. / Haag-Diergarten, S. / Urmann, M. / Wendler, W.
History
DepositionNov 19, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA
B: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6556
Polymers65,9922
Non-polymers1,6634
Water00
1
A: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8283
Polymers32,9961
Non-polymers8312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8283
Polymers32,9961
Non-polymers8312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.368, 93.218, 97.473
Angle α, β, γ (deg.)90.00, 97.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA / NUCI / NUCLEAR HORMONE RECEPTOR 1 / NUCLEAR RECEPTOR SUBFAMILY 1 GROUP C MEMBER 2 / PEROXISOME ...NUCI / NUCLEAR HORMONE RECEPTOR 1 / NUCLEAR RECEPTOR SUBFAMILY 1 GROUP C MEMBER 2 / PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR BETA / PPAR-DELTA / NUC1 / PPAR-BETA


Mass: 32996.246 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 165-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03181
#2: Chemical ChemComp-08S / 3-CHLORO-6-FLUORO-N-[2-[4-[(5-PROPAN-2-YL-1,3,4-THIADIAZOL-2-YL)SULFAMOYL]PHENYL]ETHYL]-1-BENZOTHIOPHENE-2-CARBOXAMIDE


Mass: 539.066 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H20ClFN4O3S3
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


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
Sequence detailsNTERMINAL HIS-TAG

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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: 2.91 Å3/Da / Density % sol: 57.42 % / Description: NONE
Crystal growpH: 7
Details: PEG8000 8%,BISTRISPROPANE 40MM, PH7, PROPANEDIOL 5%, KCL 300MM, DTT 5MM, EDTA 1MM, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.14→96.67 Å / Num. obs: 12270 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 80.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.8
Reflection shellResolution: 3.14→3.31 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 5.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.9.3refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE STRUCTURE

Resolution: 3.14→14.99 Å / Cor.coef. Fo:Fc: 0.9233 / Cor.coef. Fo:Fc free: 0.8476 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.442
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 581 4.79 %RANDOM
Rwork0.1878 ---
obs0.1906 12134 99.65 %-
Displacement parametersBiso mean: 57.17 Å2
Baniso -1Baniso -2Baniso -3
1-1.3712 Å20 Å20.9325 Å2
2---0.6907 Å20 Å2
3----0.6805 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: LAST / Resolution: 3.14→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 108 0 4352
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014448HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.166012HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1540SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes628HARMONIC5
X-RAY DIFFRACTIONt_it4448HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion21.83
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion582SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5227SEMIHARMONIC4
LS refinement shellResolution: 3.14→3.44 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2651 143 4.97 %
Rwork0.2035 2733 -
all0.2066 2876 -
obs--99.65 %

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