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- PDB-3et2: Structure of PPARdelta with 3-[5-Methoxy-1-(4-methoxy-benzenesulf... -

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Basic information

Entry
Database: PDB / ID: 3et2
TitleStructure of PPARdelta with 3-[5-Methoxy-1-(4-methoxy-benzenesulfonyl)-1H-indol-3-yl]-propionic acid
ComponentsPeroxisome proliferator-activated receptor delta
KeywordsTRANSCRIPTION / PPAR / PPARd / PPARdelta / Drug Discovery / Diabetes / adiponectin / metabolic disease / fragment-based drug discovery / scaffold-based drug discovery / Activator / Alternative splicing / DNA-binding / Metal-binding / Nucleus / Receptor / Transcription regulation / Zinc / Zinc-finger / K.Zhang / Wed Oct 1 17:27:09 2008 on nod
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 / 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 / glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process / Carnitine metabolism / negative regulation of myoblast differentiation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of fatty acid metabolic process / cell-substrate adhesion / fatty acid beta-oxidation / negative regulation of cholesterol storage / cellular response to nutrient levels / decidualization / keratinocyte proliferation / positive regulation of fat cell differentiation / fatty acid transport / adipose tissue development / energy homeostasis / embryo implantation / hormone-mediated signaling pathway / cholesterol metabolic process / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of miRNA transcription / fatty acid metabolic process / generation of precursor metabolites and energy / apoptotic signaling pathway / wound healing / lipid metabolic process / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / Nuclear Receptor transcription pathway / glucose metabolic process / nuclear receptor activity / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / cellular response to hypoxia / DNA-binding transcription factor binding / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / lipid binding / apoptotic process / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / 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. / c4 zinc finger in nuclear hormone receptors ...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
1-BUTANOL / Chem-ET1 / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsZhang, K.Y.J. / Wang, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Scaffold-based discovery of indeglitazar, a PPAR pan-active anti-diabetic agent
Authors: Artis, D.R. / Lin, J.J. / Zhang, C. / Wang, W. / Mehra, U. / Perreault, M. / Erbe, D. / Krupka, H.I. / England, B.P. / Arnold, J. / Plotnikov, A.N. / Marimuthu, A. / Nguyen, H. / Will, S. / ...Authors: Artis, D.R. / Lin, J.J. / Zhang, C. / Wang, W. / Mehra, U. / Perreault, M. / Erbe, D. / Krupka, H.I. / England, B.P. / Arnold, J. / Plotnikov, A.N. / Marimuthu, A. / Nguyen, H. / Will, S. / Signaevsky, M. / Kral, J. / Cantwell, J. / Settachatgull, C. / Yan, D.S. / Fong, D. / Oh, A. / Shi, S. / Womack, P. / Powell, B. / Habets, G. / West, B.L. / Zhang, K.Y. / Milburn, M.V. / Vlasuk, G.P. / Hirth, K.P. / Nolop, K. / Bollag, G. / Ibrahim, P.N. / Tobin, J.F.
History
DepositionOct 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell
Item: _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all
Revision 1.3Sep 6, 2023Group: 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_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

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)66,8807
Polymers65,8782
Non-polymers1,0015
Water6,702372
1
A: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5515
Polymers32,9391
Non-polymers6124
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)33,3292
Polymers32,9391
Non-polymers3891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.402, 94.353, 97.183
Angle α, β, γ (deg.)90.00, 98.27, 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 receptor subfamily 1 group C member 2 / Nuclear hormone receptor ...PPAR-delta / PPAR- beta / Nuclear receptor subfamily 1 group C member 2 / Nuclear hormone receptor 1 / NUC1 / NUCI


Mass: 32939.195 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARD, NR1C2, PPARB / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q03181
#2: Chemical ChemComp-ET1 / 3-{5-methoxy-1-[(4-methoxyphenyl)sulfonyl]-1H-indol-3-yl}propanoic acid


Mass: 389.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19NO6S
#3: Chemical ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 277 K / pH: 7.5
Details: The purified PPARd LBD protein was diluted to 10mg/ml and 1mM of indeglitazar was added to the diluted protein prior to crystallization by mixing equal volumes of protein/compound sample ...Details: The purified PPARd LBD protein was diluted to 10mg/ml and 1mM of indeglitazar was added to the diluted protein prior to crystallization by mixing equal volumes of protein/compound sample with reservoir solution containing 16% PEG 3350, 0.1 M Tris buffer at pH 7.5, 0.2 M magnesium chloride, and 1% n-butanol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 4, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. obs: 33526 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.098
Reflection shellResolution: 2.24→2.3 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1 / Num. unique all: 4927 / Rsym value: 0.489

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Processing

Software
NameClassification
Blu-Icedata collection
CCP4model building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GWX

1gwx


Resolution: 2.24→38.99 Å / SU ML: 0.33 / σ(F): 1.35 / Phase error: 25.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 1689 5.05 %
Rwork0.185 --
obs0.188 33474 98.7 %
all-33911 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.52 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7778 Å20 Å22.334 Å2
2--7.1072 Å2-0 Å2
3----8.8198 Å2
Refinement stepCycle: LAST / Resolution: 2.24→38.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4287 0 69 372 4728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d04451
X-RAY DIFFRACTIONf_angle_d1.086016
X-RAY DIFFRACTIONf_dihedral_angle_d16.821660
X-RAY DIFFRACTIONf_chiral_restr0.06678
X-RAY DIFFRACTIONf_plane_restr0754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.30590.30921370.25732680X-RAY DIFFRACTION100
2.3059-2.38030.29991270.22982640X-RAY DIFFRACTION99
2.3803-2.46540.30341460.22352685X-RAY DIFFRACTION100
2.4654-2.56410.26741240.20832651X-RAY DIFFRACTION99
2.5641-2.68080.27641200.20062686X-RAY DIFFRACTION100
2.6808-2.82210.29431500.19462670X-RAY DIFFRACTION100
2.8221-2.99880.25191400.19342665X-RAY DIFFRACTION100
2.9988-3.23030.2631440.17742655X-RAY DIFFRACTION99
3.2303-3.55510.21511590.15432631X-RAY DIFFRACTION99
3.5551-4.06910.1661470.13252624X-RAY DIFFRACTION98
4.0691-5.12480.20031560.13642637X-RAY DIFFRACTION98
5.1248-38.99820.24261390.18782561X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1063-0.0732-0.47890.74230.33160.7903-0.00060.0636-0.05730.0714-0.00610.04930.0129-0.04890.05920.0512-0.0093-0.01080.058-0.00820.082627.59268.627266.2076
20.9719-0.27880.11970.65750.26641.00440.0361-0.0436-0.030.01220.0364-0.0155-0.1224-0.0893-00.19280.0040.00760.14990.00090.151425.16347.019277.3455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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