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- PDB-3kdu: Crystal structure of peroxisome proliferator-activatedeceptor alp... -

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Entry
Database: PDB / ID: 3kdu
TitleCrystal structure of peroxisome proliferator-activatedeceptor alpha (PPARalpha) complex with N-3-((2-(4-Chlorophenyl)-5-methyl-1,3-oxazol-4-yl)methoxy)benzyl)-N-((4-methylphenoxy)carbonyl)glycine
ComponentsPeroxisome proliferator-activated receptor alpha
KeywordsHORMONE RECEPTOR / Nuclear Hormone Receptor / transcription regulation / Activator / DNA-binding / Lipid-binding / Receptor / Transcription
Function / homology
Function and homology information


positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / lipoprotein metabolic process / regulation of fatty acid metabolic process / positive regulation of fatty acid oxidation / cellular response to fructose stimulus / regulation of ketone metabolic process / behavioral response to nicotine ...positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / lipoprotein metabolic process / regulation of fatty acid metabolic process / positive regulation of fatty acid oxidation / cellular response to fructose stimulus / regulation of ketone metabolic process / behavioral response to nicotine / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / negative regulation of hepatocyte apoptotic process / mitogen-activated protein kinase kinase kinase binding / negative regulation of leukocyte cell-cell adhesion / ubiquitin conjugating enzyme binding / negative regulation of glycolytic process / negative regulation of sequestering of triglyceride / nuclear steroid receptor activity / DNA-binding transcription activator activity / nitric oxide metabolic process / positive regulation of fatty acid metabolic process / NFAT protein binding / positive regulation of ATP biosynthetic process / negative regulation of cholesterol storage / negative regulation of macrophage derived foam cell differentiation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of cytokine production involved in inflammatory response / epidermis development / phosphatase binding / positive regulation of lipid biosynthetic process / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / negative regulation of reactive oxygen species biosynthetic process / positive regulation of gluconeogenesis / negative regulation of signaling receptor activity / MDM2/MDM4 family protein binding / RORA activates gene expression / negative regulation of blood pressure / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / cellular response to starvation / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian gene expression / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / gluconeogenesis / fatty acid metabolic process / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / wound healing / SUMOylation of intracellular receptors / Heme signaling / response to insulin / regulation of circadian rhythm / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription coactivator binding / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / nuclear receptor activity / Circadian Clock / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / lipid binding / protein-containing complex binding / 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 alpha / 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 alpha / 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-NKS / Peroxisome proliferator-activated receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.07 Å
AuthorsMuckelbauer, J.K.
Citation
Journal: J.Med.Chem. / Year: 2010
Title: Discovery of an oxybenzylglycine based peroxisome proliferator activated receptor alpha selective agonist 2-((3-((2-(4-chlorophenyl)-5-methyloxazol-4-yl)methoxy)benzyl)(methoxycarbonyl)amino) ...Title: Discovery of an oxybenzylglycine based peroxisome proliferator activated receptor alpha selective agonist 2-((3-((2-(4-chlorophenyl)-5-methyloxazol-4-yl)methoxy)benzyl)(methoxycarbonyl)amino)acetic acid (BMS-687453).
Authors: Li, J. / Kennedy, L.J. / Shi, Y. / Tao, S. / Ye, X.Y. / Chen, S.Y. / Wang, Y. / Hernandez, A.S. / Wang, W. / Devasthale, P.V. / Chen, S. / Lai, Z. / Zhang, H. / Wu, S. / Smirk, R.A. / ...Authors: Li, J. / Kennedy, L.J. / Shi, Y. / Tao, S. / Ye, X.Y. / Chen, S.Y. / Wang, Y. / Hernandez, A.S. / Wang, W. / Devasthale, P.V. / Chen, S. / Lai, Z. / Zhang, H. / Wu, S. / Smirk, R.A. / Bolton, S.A. / Ryono, D.E. / Zhang, H. / Lim, N.K. / Chen, B.C. / Locke, K.T. / O'Malley, K.M. / Zhang, L. / Srivastava, R.A. / Miao, B. / Meyers, D.S. / Monshizadegan, H. / Search, D. / Grimm, D. / Zhang, R. / Harrity, T. / Kunselman, L.K. / Cap, M. / Kadiyala, P. / Hosagrahara, V. / Zhang, L. / Xu, C. / Li, Y.X. / Muckelbauer, J.K. / Chang, C. / An, Y. / Krystek, S.R. / Blanar, M.A. / Zahler, R. / Mukherjee, R. / Cheng, P.T. / Tino, J.A.
#1: Journal: To be Published
Title: Synthesis and Structure-Activity Relationships of 2-Aryl-4-oxazolylmethoxy Benzylglycines and 2-Aryl-4-thiazolylmethoxy Benzylglycines as Novel, Potent PPARalpha Selective Activators-PPARalpha ...Title: Synthesis and Structure-Activity Relationships of 2-Aryl-4-oxazolylmethoxy Benzylglycines and 2-Aryl-4-thiazolylmethoxy Benzylglycines as Novel, Potent PPARalpha Selective Activators-PPARalpha and PPARgamma Selective Modulation
Authors: Ye, X.-Y. / Chen, S. / Zhang, H. / Locke, K.T. / O'Malley, K. / Zhang, L. / Srivastava, R. / Miao, B. / Meyers, D. / Monshizadegan, H. / Search, D. / Grimm, D. / Zhang, R. / Lippy, J. / ...Authors: Ye, X.-Y. / Chen, S. / Zhang, H. / Locke, K.T. / O'Malley, K. / Zhang, L. / Srivastava, R. / Miao, B. / Meyers, D. / Monshizadegan, H. / Search, D. / Grimm, D. / Zhang, R. / Lippy, J. / Twamley, C. / Muckelbauer, J.K. / Chang, C. / An, Y. / Hosagrahara, V. / Zhang, L. / Yang, T.-J. / Mukherjee, R. / Cheng, P.T.W. / Tino, J.A.
History
DepositionOct 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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

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Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor alpha
B: Peroxisome proliferator-activated receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6754
Polymers62,6332
Non-polymers1,0422
Water7,800433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peroxisome proliferator-activated receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8372
Polymers31,3161
Non-polymers5211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Peroxisome proliferator-activated receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8372
Polymers31,3161
Non-polymers5211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.930, 63.930, 126.771
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Peroxisome proliferator-activated receptor alpha / PPAR-alpha / Nuclear receptor subfamily 1 group C member 1


Mass: 31316.445 Da / Num. of mol.: 2 / Fragment: Ligand-binding domain: UNP residues 196-468
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARA, NR1C1, PPAR / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07869
#2: Chemical ChemComp-NKS / N-(3-{[2-(4-chlorophenyl)-5-methyl-1,3-oxazol-4-yl]methoxy}benzyl)-N-[(4-methylphenoxy)carbonyl]glycine


Type: L-peptide linking / Mass: 520.961 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H25ClN2O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: PEG 4000, Ammonium and magnesium acetate, VAPOR DIFFUSION, temperature 298K
PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 30861 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 25.1
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 5.6 / Rsym value: 0.321 / % possible all: 99.2

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3KDT

3kdt


Resolution: 2.07→45.22 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.908 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.863 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1551 5 %RANDOM
Rwork0.178 ---
obs0.181 30819 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.15 Å2 / Biso mean: 21.392 Å2 / Biso min: 7.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.07→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4188 0 74 433 4695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224458
X-RAY DIFFRACTIONr_angle_refined_deg1.0511.996045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4495564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37825.078193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94815818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0171517
X-RAY DIFFRACTIONr_chiral_restr0.0750.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023325
X-RAY DIFFRACTIONr_nbd_refined0.1890.22144
X-RAY DIFFRACTIONr_nbtor_refined0.2960.23118
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2377
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.225
X-RAY DIFFRACTIONr_mcbond_it0.6441.52831
X-RAY DIFFRACTIONr_mcangle_it1.04624417
X-RAY DIFFRACTIONr_scbond_it1.48131831
X-RAY DIFFRACTIONr_scangle_it2.1964.51609
LS refinement shellResolution: 2.07→2.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 103 -
Rwork0.203 2150 -
all-2253 -
obs--100 %

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