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- PDB-3oz0: PPAR Delta in complex with azppard02 -

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Basic information

Entry
Database: PDB / ID: 3oz0
TitlePPAR Delta in complex with azppard02
ComponentsPeroxisome proliferator-activated receptor delta
KeywordsTRANSCRIPTION/TRANSCRIPTION REGULATOR / TRANSCRIPTION FACTOR / TRANSCRIPTION / NUCLEAR RECEPTOR FOLD / TRANSCRIPTION REGULATION / TRANSCRIPTION-TRANSCRIPTION REGULATOR complex
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-3OZ / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3 Å
AuthorsOgg, D.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Discovery of isoindoline and tetrahydroisoquinoline derivatives as potent, selective PPARδ agonists
Authors: Luckhurst, C.A. / Stein, L.A. / Furber, M. / Webb, N. / Ratcliffe, M.J. / Allenby, G. / Botterell, S. / Tomlinson, W. / Martin, B. / Walding, A.
History
DepositionSep 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 29, 2012Group: Structure summary
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1662
Polymers32,6811
Non-polymers4851
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.258, 49.134, 58.574
Angle α, β, γ (deg.)90.00, 105.34, 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


Mass: 32680.836 Da / Num. of mol.: 1 / Fragment: Nuclear receptor protein, UNP residues 165-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARD, NR1C2, PPARB / Production host: Escherichia coli (E. coli) / References: UniProt: Q03181
#2: Chemical ChemComp-3OZ / [4-({(1S)-1-[(2,4-dichlorophenyl)carbamoyl]-1,3-dihydro-2H-isoindol-2-yl}methyl)-2-methylphenoxy]acetic acid


Mass: 485.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H22Cl2N2O4

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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: 2.4 Å3/Da / Density % sol: 48.85 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9134 / Wavelength: 0.9134 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2009 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9134 Å / Relative weight: 1
ReflectionResolution: 3→56.49 Å / Num. all: 6381 / Num. obs: 6381 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.7
Reflection shellResolution: 3→3.24 Å / Redundancy: 3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.3 / % possible all: 95.2

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Processing

Software
NameVersionClassification
RemDAqdata collection
MOLREPphasing
REFMAC5.2.0005refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: 2GWX

2gwx


Resolution: 3→56.49 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.861 / SU B: 21.567 / SU ML: 0.391 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.529 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27048 536 8.9 %RANDOM
Rwork0.21478 ---
all0.22412 5457 --
obs0.21977 5457 93.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.81 Å2
Baniso -1Baniso -2Baniso -3
1-3.73 Å20 Å24.08 Å2
2---2.05 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 3→56.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 33 0 2134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0222137
X-RAY DIFFRACTIONr_bond_other_d0.0010.021976
X-RAY DIFFRACTIONr_angle_refined_deg0.8251.982902
X-RAY DIFFRACTIONr_angle_other_deg0.69334568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2715258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.21924.1392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57515360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1741510
X-RAY DIFFRACTIONr_chiral_restr0.0440.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022337
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02438
X-RAY DIFFRACTIONr_nbd_refined0.1770.2516
X-RAY DIFFRACTIONr_nbd_other0.150.21964
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21079
X-RAY DIFFRACTIONr_nbtor_other0.0820.21107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.242
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0910.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1460.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7821705
X-RAY DIFFRACTIONr_mcbond_other0.0942519
X-RAY DIFFRACTIONr_mcangle_it0.93332103
X-RAY DIFFRACTIONr_scbond_it1.2764988
X-RAY DIFFRACTIONr_scangle_it1.9296799
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.001→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 46 -
Rwork0.311 404 -
obs--92.59 %

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