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- PDB-3peq: PPARd complexed with a phenoxyacetic acid partial agonist -

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Basic information

Entry
Database: PDB / ID: 3peq
TitlePPARd complexed with a phenoxyacetic acid partial agonist
ComponentsPeroxisome proliferator-activated receptor delta
KeywordsTRANSCRIPTION/TRANSCRIPTION agonist / PPAR nuclear receptor / TRANSCRIPTION-TRANSCRIPTION agonist 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 / regulation of skeletal muscle satellite cell proliferation / axon ensheathment / 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 / regulation of skeletal muscle satellite cell proliferation / axon ensheathment / glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process / negative regulation of myoblast differentiation / Carnitine metabolism / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / nuclear steroid receptor activity / fatty acid beta-oxidation / positive regulation of fatty acid metabolic process / cell-substrate adhesion / 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 / cholesterol metabolic process / hormone-mediated signaling pathway / fatty acid metabolic process / negative regulation of miRNA transcription / phosphatidylinositol 3-kinase/protein kinase B signal transduction / generation of precursor metabolites and energy / apoptotic signaling pathway / wound healing / lipid metabolic process / transcription coactivator binding / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / 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 / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / chromatin / positive regulation of gene expression / 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
Chem-3EQ / IODIDE ION / hexyl beta-D-glucopyranoside / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLambert, M.H. / Evans, K.A. / Shearer, B.G. / Wisnoski, D.D. / Shi, D. / Jin, J. / Rivero, R.A. / Sparks, S.M. / Winegar, D.A. / Billin, A.N. ...Lambert, M.H. / Evans, K.A. / Shearer, B.G. / Wisnoski, D.D. / Shi, D. / Jin, J. / Rivero, R.A. / Sparks, S.M. / Winegar, D.A. / Billin, A.N. / Britt, C. / Way, J.M. / Leesnitzer, L.M. / Merrihew, R.V.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Phenoxyacetic acid PPARd partial agonists for the treatment of type 2 diabetes: synthesis, optimization, and in vivo efficacy
Authors: Evans, K.A. / Shearer, B.G. / Wisnoski, D.D. / Shi, D. / Sparks, S.M. / Sternbach, D.D. / Winegar, D.A. / Billin, A.N. / Britt, C. / Way, J.M. / Epperly, A.H. / Leesnitzer, L.M. / Merrihew, ...Authors: Evans, K.A. / Shearer, B.G. / Wisnoski, D.D. / Shi, D. / Sparks, S.M. / Sternbach, D.D. / Winegar, D.A. / Billin, A.N. / Britt, C. / Way, J.M. / Epperly, A.H. / Leesnitzer, L.M. / Merrihew, R.V. / Xu, R.X. / Lambert, M.H. / Jin, J.
History
DepositionOct 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.mon_nstd_flag / _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 6, 2023Group: 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

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)64,68813
Polymers62,0342
Non-polymers2,65411
Water3,009167
1
A: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6038
Polymers31,0171
Non-polymers1,5867
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0855
Polymers31,0171
Non-polymers1,0684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Peroxisome proliferator-activated receptor delta
hetero molecules

B: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,68813
Polymers62,0342
Non-polymers2,65411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area2780 Å2
ΔGint-17 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.472, 95.535, 96.537
Angle α, β, γ (deg.)90.00, 97.76, 90.00
Int Tables number4
Space group name H-MP1211

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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: 31017.061 Da / Num. of mol.: 2 / Fragment: unp residues 171-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1C2, PPARB, PPARD / Plasmid: pRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q03181
#2: Chemical ChemComp-3EQ / [(4-{butyl[2-methyl-4'-(methylsulfanyl)biphenyl-3-yl]sulfamoyl}naphthalen-1-yl)oxy]acetic acid


Mass: 549.701 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H31NO5S2
#3: Sugar ChemComp-JZR / hexyl beta-D-glucopyranoside / hexyl beta-D-glucoside / hexyl D-glucoside / hexyl glucoside


Type: D-saccharide / Mass: 264.315 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H24O6
#4: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 3.03 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 mM potassium iodide, 20% PEG3350, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 12, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30.26 Å / Num. all: 25794 / Num. obs: 25794 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 17
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2 / Num. unique all: 1891 / % possible all: 94.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1gwx

1gwx


Resolution: 2.4→30.26 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.937 / SU B: 14.3 / SU ML: 0.17 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23667 1390 5.1 %RANDOM
Rwork0.19872 ---
obs0.20064 25794 97.56 %-
all-25794 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.361 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20.58 Å2
2--2.36 Å20 Å2
3----2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4064 0 136 167 4367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224320
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.9955860
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7045517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2724.14186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43515730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2371521
X-RAY DIFFRACTIONr_chiral_restr0.0670.2675
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213279
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3641.52587
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.71524174
X-RAY DIFFRACTIONr_scbond_it1.04231733
X-RAY DIFFRACTIONr_scangle_it1.7784.51681
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 108 -
Rwork0.236 1891 -
obs-1891 94.78 %
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)
12.72040.3096-0.79252.26290.33643.3815-0.03880.1493-0.1580.07590.04970.0651-0.0203-0.2326-0.0110.04840.0001-0.01850.0241-0.00090.051128.1668.12866.163
22.22860.55130.08262.058-1.10417.0576-0.00320.08470.1409-0.05760.09380.0418-0.46070.3365-0.09060.1892-0.03720.03840.0342-0.01390.04510.048-1.62918.924
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A209 - 475
2X-RAY DIFFRACTION2B209 - 477

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