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- PDB-7qb1: PPARg in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 7qb1
TitlePPARg in complex with inhibitor
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsNUCLEAR PROTEIN / Nuclear hormone receptor CDK9
Function / homology
Function and homology information


prostaglandin receptor activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / positive regulation of cholesterol transport / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of low-density lipoprotein receptor activity ...prostaglandin receptor activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / positive regulation of cholesterol transport / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of low-density lipoprotein receptor activity / arachidonate binding / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / DNA binding domain binding / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / WW domain binding / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / LBD domain binding / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / E-box binding / alpha-actinin binding / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / white fat cell differentiation / negative regulation of BMP signaling pathway / cell fate commitment / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / negative regulation of MAPK cascade / BMP signaling pathway / retinoic acid receptor signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cell maturation / epithelial cell differentiation / negative regulation of signaling receptor activity / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / regulation of cellular response to insulin stimulus / negative regulation of angiogenesis / response to nutrient / negative regulation of miRNA transcription / Regulation of PTEN gene transcription / transcription coregulator binding / fatty acid metabolic process / negative regulation of smooth muscle cell proliferation / positive regulation of apoptotic signaling pathway / negative regulation of transforming growth factor beta receptor signaling pathway / peptide binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / regulation of circadian rhythm / placenta development / PPARA activates gene expression / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / positive regulation of miRNA transcription / regulation of blood pressure / cellular response to insulin stimulus / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / rhythmic process / glucose homeostasis / cellular response to hypoxia / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / intracellular membrane-bounded organelle / innate immune response / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression
Similarity search - Function
Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated 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 gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated 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
Similarity search - Domain/homology
Chem-9WQ / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPetersen, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2022
Title: Discovery by Virtual Screening of an Inhibitor of CDK5-Mediated PPAR gamma Phosphorylation.
Authors: O'Mahony, G. / Petersen, J. / Ek, M. / Rae, R. / Johansson, C. / Jianming, L. / Prokoph, N. / Bergstrom, F. / Bamberg, K. / Giordanetto, F. / Zarrouki, B. / Karlsson, D. / Hogner, A.
History
DepositionNov 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Peroxisome proliferator-activated receptor gamma
BBB: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4626
Polymers65,3882
Non-polymers1,0754
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-32 kcal/mol
Surface area24950 Å2
Unit cell
Length a, b, c (Å)93.368, 60.664, 118.254
Angle α, β, γ (deg.)90.000, 102.934, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peroxisome proliferator-activated receptor gamma / PPAR-gamma / Nuclear receptor subfamily 1 group C member 3


Mass: 32693.824 Da / Num. of mol.: 2 / Fragment: UNP residues 195-477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli (E. coli) / References: UniProt: P37231
#2: Chemical ChemComp-9WQ / 3-[(3,4-dichlorophenyl)methyl]-4-oxidanylidene-6-phenoxy-phthalazine-1-carboxylic acid


Mass: 441.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H14Cl2N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20mM Tris pH 8.0, 5mM DTT, 100mM NaCl , 2mM EDTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jul 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 34961 / % possible obs: 99.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.2
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.67 / Num. unique obs: 4068

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: internal modle

Resolution: 2.2→45.982 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.106 / SU ML: 0.175 / Cross valid method: FREE R-VALUE / ESU R: 0.253 / ESU R Free: 0.21
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2494 1626 4.971 %
Rwork0.1985 31081 -
all0.201 --
obs-32707 99.091 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 59.746 Å2
Baniso -1Baniso -2Baniso -3
1-0.124 Å2-0 Å2-0.092 Å2
2---0.217 Å2-0 Å2
3---0.122 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4170 0 70 78 4318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134378
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174297
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.6595905
X-RAY DIFFRACTIONr_angle_other_deg1.3381.5839929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4265527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12524.049205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.81215845
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0461517
X-RAY DIFFRACTIONr_chiral_restr0.080.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024829
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02903
X-RAY DIFFRACTIONr_nbd_refined0.2210.21020
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.23930
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22102
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22065
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2118
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0410.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2270.221
X-RAY DIFFRACTIONr_nbd_other0.1740.2105
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.29
X-RAY DIFFRACTIONr_mcbond_it5.4845.862114
X-RAY DIFFRACTIONr_mcbond_other5.485.8552113
X-RAY DIFFRACTIONr_mcangle_it7.3938.7552636
X-RAY DIFFRACTIONr_mcangle_other7.3928.7612637
X-RAY DIFFRACTIONr_scbond_it6.9976.6442264
X-RAY DIFFRACTIONr_scbond_other6.9446.6342223
X-RAY DIFFRACTIONr_scangle_it10.0539.6563268
X-RAY DIFFRACTIONr_scangle_other9.9979.6373209
X-RAY DIFFRACTIONr_lrange_it12.27769.9194879
X-RAY DIFFRACTIONr_lrange_other12.24670.0674822
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.2-2.2570.3431280.31122600.31324300.7270.74298.27160.282
2.257-2.3190.3071050.26122630.26323930.8120.83298.95530.236
2.319-2.3860.3191020.23921270.24222620.8350.8798.54110.212
2.386-2.4590.3061010.22421010.22722230.8380.8999.05530.194
2.459-2.5390.229940.19520560.19621630.9060.91299.3990.165
2.539-2.6280.289900.2119940.21421030.8820.90599.09650.183
2.628-2.7270.28800.20718910.2119960.8770.90898.74750.179
2.727-2.8380.302940.19418350.19919410.8870.92499.38180.17
2.838-2.9640.2661090.20217570.20618770.8980.91799.4140.176
2.964-3.1080.3131010.21316980.21918040.8620.90799.72280.19
3.108-3.2750.272830.20516030.20916880.8920.92499.88150.187
3.275-3.4720.259790.19415270.19716200.9130.93699.13580.184
3.472-3.7110.255790.1914220.19415160.9340.94699.01060.184
3.711-4.0060.203780.16813230.1714100.9460.95599.36170.167
4.006-4.3850.181730.15712160.15812990.9530.95999.23020.158
4.385-4.8970.209620.16211170.16511860.9540.95899.40980.164
4.897-5.6440.244530.19610000.19910650.9290.94298.87320.2
5.644-6.8860.271540.2168370.2198960.8990.92799.4420.214
6.886-9.6310.186430.1926530.1917020.9510.95599.14530.202
9.631-45.9820.324180.2514010.2544290.920.94297.6690.296

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