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

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Entry
Database: PDB / ID: 2xyj
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
Function / homology
Function and homology information


positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / fat cell proliferation / 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 fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / fat cell proliferation / 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 / proteoglycan metabolic process / fatty acid catabolic process / negative regulation of collagen biosynthetic process / positive regulation of myoblast proliferation / 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 / negative regulation of cholesterol storage / fatty acid beta-oxidation / cell-substrate adhesion / energy homeostasis / decidualization / nuclear steroid receptor activity / keratinocyte proliferation / positive regulation of fat cell differentiation / NF-kappaB binding / adipose tissue development / positive regulation of insulin secretion involved in cellular response to glucose stimulus / response to glucose / fatty acid transport / cellular response to nutrient levels / cholesterol metabolic process / intracellular receptor signaling pathway / hormone-mediated signaling pathway / embryo implantation / negative regulation of miRNA transcription / response to activity / generation of precursor metabolites and energy / negative regulation of smooth muscle cell proliferation / apoptotic signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / fatty acid metabolic process / wound healing / negative regulation of cell growth / Nuclear Receptor transcription pathway / lipid metabolic process / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / vasodilation / transcription coactivator binding / nuclear receptor activity / glucose metabolic process / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / 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-WLM / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 18, 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 1.3Oct 16, 2019Group: Data collection / Other / Category: pdbx_database_status / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Revision 1.4May 1, 2024Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA
B: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2117
Polymers65,9922
Non-polymers2,2185
Water1,874104
1
A: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2254
Polymers32,9961
Non-polymers1,2283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9863
Polymers32,9961
Non-polymers9902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.749, 112.009, 152.573
Angle α, β, γ (deg.)90.00, 95.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


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-WLM / 5-CHLORO-2-METHOXY-N-[2-[4-[(5-PROPAN-2-YL-1,3,4-THIADIAZOL-2-YL)SULFAMOYL]PHENYL]ETHYL]BENZAMIDE


Mass: 495.015 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H23ClN4O4S2
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.58 Å3/Da / Density % sol: 51.9 % / Description: NONE
Crystal growpH: 8 / Details: PEG3350 11%, TRIS 100MM PH 8, CACL2 300MM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→37.5 Å / Num. obs: 28063 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameClassification
BUSTER-TNTrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE STRUCTURE

Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 204-207 AND 229-233 ARE NOT VISIBLE. LIGAND MOLECULES 3 AND 4 ARE AT THE INTERFACE BETWEEN PROTEINS A AND B.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2321 8 %RANDOM
Rwork0.208 ---
obs-28022 99.9 %-
Displacement parametersBiso mean: 43.9 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4202 0 144 104 4450

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