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- PDB-2j14: 3,4,5-Trisubstituted Isoxazoles as Novel PPARdelta Agonists: Part2 -

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Basic information

Entry
Database: PDB / ID: 2j14
Title3,4,5-Trisubstituted Isoxazoles as Novel PPARdelta Agonists: Part2
ComponentsPEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA
KeywordsTRANSCRIPTION / NUCLEAR RECEPTOR FOLD / TRANSCRIPTION REGULATION / PPAR / ZINC / RECEPTOR / ACTIVATOR / FATTY ACIDS / NUCLEAR PROTEIN / ALTERNATIVE SPLICING / ZINC-FINGER / DNA-BINDING / METAL-BINDING
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 / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / D-glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process ...fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / D-glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process / negative regulation of myoblast differentiation / Carnitine shuttle / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of fatty acid metabolic process / fatty acid beta-oxidation / cell-substrate adhesion / negative regulation of cholesterol storage / decidualization / keratinocyte proliferation / positive regulation of fat cell differentiation / adipose tissue development / cellular response to nutrient levels / fatty acid transport / energy homeostasis / embryo implantation / cholesterol metabolic process / hormone-mediated signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of miRNA transcription / apoptotic signaling pathway / generation of precursor metabolites and energy / fatty acid metabolic process / wound healing / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription coactivator binding / negative regulation of inflammatory response / Nuclear Receptor transcription pathway / nuclear receptor activity / negative regulation of epithelial cell proliferation / glucose metabolic process / sequence-specific double-stranded DNA binding / cellular response to hypoxia / DNA-binding transcription factor binding / cell population proliferation / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / lipid binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / apoptotic process / 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 / Zinc finger, C4 type (two domains) / 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 / Zinc finger, C4 type (two domains) / 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-GNI / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsEpple, R. / Azimioara, M. / Russo, R. / Xie, Y. / Wang, X. / Cow, C. / Wityak, J. / Karanewsky, D. / Bursulaya, B. / Kreusch, A. ...Epple, R. / Azimioara, M. / Russo, R. / Xie, Y. / Wang, X. / Cow, C. / Wityak, J. / Karanewsky, D. / Bursulaya, B. / Kreusch, A. / Tuntland, T. / Gerken, A. / Iskandar, M. / Saez, E. / Seidel, H.M. / Tian, S.S.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: 3,4,5-Trisubstituted Isoxazoles as Novel Ppardelta Agonists. Part 2
Authors: Epple, R. / Azimioara, M. / Russo, R. / Xie, Y. / Wang, X. / Cow, C. / Wityak, J. / Karanewsky, D. / Bursulaya, B. / Kreusch, A. / Tuntland, T. / Gerken, A. / Iskandar, M. / Saez, E. / Seidel, H.M. / Tian, S.S.
History
DepositionAug 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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

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)66,3844
Polymers65,3622
Non-polymers1,0232
Water2,324129
1
A: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1922
Polymers32,6811
Non-polymers5111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1922
Polymers32,6811
Non-polymers5111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)39.376, 93.390, 92.258
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA / PPAR-DELTA / PPAR-BETA / NUCLEAR HORMONE RECEPTOR 1 / NUC1 / NUCI / PPARDELTA


Mass: 32680.836 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) / References: UniProt: Q03181
#2: Chemical ChemComp-GNI / (3-{4-[2-(2,4-DICHLORO-PHENOXY)-ETHYLCARBAMOYL]-5-PHENYL-ISOXAZOL-3-YL}-PHENYL)-ACETIC ACID


Mass: 511.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H20Cl2N2O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.6 Å3/Da / Density % sol: 52.61 %

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→46.7 Å / Num. obs: 16248 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 44.9 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 5.3
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.62 / % possible all: 96.6

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GWX

2gwx


Resolution: 2.8→46.7 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 899104.04 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: IN CHAIN A RESIDUE 207 HAS BEEN MODELLED AS ALA, NOT AS HIS DUE TO INSUFFICIENT DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.284 801 5 %RANDOM
Rwork0.224 ---
obs0.224 16148 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.9417 Å2 / ksol: 0.382535 e/Å3
Displacement parametersBiso mean: 35.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.82 Å20 Å20 Å2
2---10.9 Å20 Å2
3---15.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.8→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4074 0 70 129 4273
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.42 135 5.1 %
Rwork0.351 2498 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4NVP_LCI765.PARAMNVP_LCI765.TOP

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