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

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Entry
Database: PDB / ID: 3kdt
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-(methoxycarbonyl)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 / regulation of ketone metabolic process / regulation of fatty acid metabolic process / cellular response to fructose stimulus / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / 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 / regulation of ketone metabolic process / regulation of fatty acid metabolic process / cellular response to fructose stimulus / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / behavioral response to nicotine / lipoprotein metabolic process / positive regulation of fatty acid oxidation / negative regulation of hepatocyte apoptotic process / negative regulation of leukocyte cell-cell adhesion / mitogen-activated protein kinase kinase kinase binding / ubiquitin conjugating enzyme binding / negative regulation of glycolytic process / negative regulation of triglyceride storage / nuclear steroid receptor activity / nitric oxide metabolic process / DNA-binding transcription activator activity / positive regulation of fatty acid metabolic process / positive regulation of ATP biosynthetic process / NFAT protein binding / negative regulation of cholesterol storage / negative regulation of macrophage derived foam cell differentiation / 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 blood pressure / negative regulation of signaling receptor activity / negative regulation of reactive oxygen species biosynthetic process / : / hormone-mediated signaling pathway / MDM2/MDM4 family protein binding / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / response to nutrient / positive regulation of gluconeogenesis / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / cellular response to starvation / gluconeogenesis / fatty acid metabolic process / response to insulin / SUMOylation of intracellular receptors / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / transcription coactivator binding / Heme signaling / wound healing / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / regulation of circadian rhythm / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear receptor activity / : / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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 / Double treble clef zinc finger, C4 type / 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 / 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-7HA / Peroxisome proliferator-activated receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)63,5234
Polymers62,6332
Non-polymers8902
Water362
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)31,7612
Polymers31,3161
Non-polymers4451
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)31,7612
Polymers31,3161
Non-polymers4451
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.754, 64.754, 123.664
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-7HA / N-(3-{[2-(4-chlorophenyl)-5-methyl-1,3-oxazol-4-yl]methoxy}benzyl)-N-(methoxycarbonyl)glycine


Type: L-peptide linking / Mass: 444.865 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H21ClN2O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 40.57 %
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: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 13931 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 17.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.429 / % possible all: 99.7

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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 / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.858 / Occupancy max: 1 / Occupancy min: 1 / SU B: 19.985 / SU ML: 0.402 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.493 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.316 691 5 %RANDOM
Rwork0.253 ---
obs0.256 13908 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.9 Å2 / Biso mean: 57.948 Å2 / Biso min: 25.85 Å2
Baniso -1Baniso -2Baniso -3
1-2.49 Å20 Å20 Å2
2--2.49 Å20 Å2
3----4.97 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 62 2 4245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224319
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.9885828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.895530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13125.081185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85615778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3351516
X-RAY DIFFRACTIONr_chiral_restr0.0820.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023196
X-RAY DIFFRACTIONr_nbd_refined0.2180.22095
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23003
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2136
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0590.21
X-RAY DIFFRACTIONr_mcbond_it0.5621.52742
X-RAY DIFFRACTIONr_mcangle_it0.9924296
X-RAY DIFFRACTIONr_scbond_it0.94431744
X-RAY DIFFRACTIONr_scangle_it1.5414.51532
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.49 49 -
Rwork0.333 941 -
all-990 -
obs--99 %

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