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- PDB-9qgj: Human PPAR-gamma ligand binding domain in complex with LW90 -

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Basic information

Entry
Database: PDB / ID: 9qgj
TitleHuman PPAR-gamma ligand binding domain in complex with LW90
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / PPAR / PPAR gamma / PPARg / peroxisome proliferator-activated receptor gamma / nuclear receptor / transcription factor / partial agonist / agonist
Function / homology
Function and homology information


prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / beige fat cell differentiation / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / arachidonate binding ...prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / beige fat cell differentiation / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / arachidonate binding / positive regulation of adiponectin secretion / DNA binding domain binding / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of cardiac muscle hypertrophy in response to stress / positive regulation of fatty acid metabolic process / STAT family protein binding / positive regulation of lipid metabolic process / WW domain binding / response to lipid / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / LBD domain binding / positive regulation of lipoprotein transport / negative regulation of SMAD protein signal transduction / lipid homeostasis / E-box binding / alpha-actinin binding / R-SMAD binding / negative regulation of blood vessel endothelial cell migration / white fat cell differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of lipid storage / positive regulation of cholesterol efflux / negative regulation of BMP signaling pathway / monocyte differentiation / cell fate commitment / BMP signaling pathway / cellular response to low-density lipoprotein particle stimulus / negative regulation of mitochondrial fission / negative regulation of osteoblast differentiation / long-chain fatty acid transport / positive regulation of fat cell differentiation / nuclear retinoid X receptor binding / fat cell differentiation / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / intracellular receptor signaling pathway / negative regulation of MAPK cascade / peptide binding / cell maturation / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / regulation of cellular response to insulin stimulus / positive regulation of adipose tissue development / response to nutrient / negative regulation of miRNA transcription / placenta development / brown fat cell differentiation / negative regulation of angiogenesis / Regulation of PTEN gene transcription / transcription coregulator binding / positive regulation of apoptotic signaling pathway / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / PPARA activates gene expression / fatty acid metabolic process / regulation of circadian rhythm / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / positive regulation of miRNA transcription / mRNA transcription by RNA polymerase II / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / regulation of blood pressure / nuclear receptor activity / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / rhythmic process / glucose homeostasis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to hypoxia / DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / signaling receptor complex / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / 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 / Double treble clef zinc finger, C4 type / 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 / 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
Similarity search - Domain/homology
: / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOerlemans, G.J.M. / Koops, A.A. / Brunsveld, L.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: To Be Published
Title: Development and characterization of novel indazole-based PPAR-gamma partial agonists
Authors: Koops, A.A. / Oerlemans, G.J.M. / Brunsveld, L.
History
DepositionMar 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,2064
Polymers62,8212
Non-polymers1,3852
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-4 kcal/mol
Surface area24130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.166, 61.582, 119.003
Angle α, β, γ (deg.)90.000, 101.820, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 233 through 251 or (resid 252...
d_2ens_1(chain "B" and (resid 233 through 243 or (resid 244...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11HISHISTHRTHRAB233 - 2693 - 39
d_12LYSLYSLYSLYSAB272 - 29142 - 61
d_13LYSLYSLYSLYSAB303 - 50273 - 272
d_14L90L90L90L90AD601
d_21HISHISSERSERBA233 - 4573 - 227
d_22LEULEULYSLYSBA459 - 502229 - 272
d_23L90L90L90L90BC601

NCS oper: (Code: givenMatrix: (0.0930961988153, 0.98237726806, 0.162074060125), (0.986889734726, -0.11260029996, 0.115627954841), (0.131839862174, 0.14918470313, -0.979980701389)Vector: 15. ...NCS oper: (Code: given
Matrix: (0.0930961988153, 0.98237726806, 0.162074060125), (0.986889734726, -0.11260029996, 0.115627954841), (0.131839862174, 0.14918470313, -0.979980701389)
Vector: 15.8127905768, -24.2236492944, 47.3282373225)

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Components

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


Mass: 31410.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal GSHM left from Thrombin cleavage / Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37231
#2: Chemical ChemComp-A1I6R / 4-[5-chloranyl-1-[2-chloranyl-6-(trifluoromethyl)phenyl]carbonyl-indazol-3-yl]-3-[[(3~{S})-1-[(2-methylpropan-2-yl)oxycarbonyl]piperidin-3-yl]methoxy]benzoic acid


Mass: 692.509 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H30Cl2F3N3O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.9M-1.2M sodium citrate tribasic dihydrate, 0.1M sodium cacodylate
PH range: 6.4-7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967697 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967697 Å / Relative weight: 1
ReflectionResolution: 2.2→58.24 Å / Num. obs: 33110 / % possible obs: 97.4 % / Redundancy: 2.8 % / Biso Wilson estimate: 50.76 Å2 / CC1/2: 0.994 / Net I/σ(I): 8.7
Reflection shellResolution: 2.2→2.27 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2835 / CC1/2: 0.735

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→58.24 Å / SU ML: 0.3595 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.9249
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2554 1638 4.96 %
Rwork0.2229 31390 -
obs0.2245 33028 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.44 Å2
Refinement stepCycle: LAST / Resolution: 2.2→58.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4006 0 94 22 4122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00884174
X-RAY DIFFRACTIONf_angle_d1.36195665
X-RAY DIFFRACTIONf_chiral_restr0.0604662
X-RAY DIFFRACTIONf_plane_restr0.0109719
X-RAY DIFFRACTIONf_dihedral_angle_d9.0842588
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.33395815746 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.4091530.35842567X-RAY DIFFRACTION96.63
2.26-2.340.34691400.31972622X-RAY DIFFRACTION97.84
2.34-2.420.29581310.31092611X-RAY DIFFRACTION97.96
2.42-2.520.31741290.2822642X-RAY DIFFRACTION98.3
2.52-2.630.34121500.26762605X-RAY DIFFRACTION97.56
2.63-2.770.31521340.25822633X-RAY DIFFRACTION97.5
2.77-2.950.32511430.2862643X-RAY DIFFRACTION97.51
2.95-3.170.33941300.27562605X-RAY DIFFRACTION97.37
3.17-3.490.27291420.23662614X-RAY DIFFRACTION96.53
3.49-40.24411090.20642567X-RAY DIFFRACTION93.86
4-5.030.18071360.17122611X-RAY DIFFRACTION96.05
5.04-58.240.21981410.18652670X-RAY DIFFRACTION95.55
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)
12.564553658860.06494311259170.3289116977631.438864183940.2696062693223.346986230130.000889910942791-0.232432448859-0.09747016281060.296054323160.08036160298780.121284423627-0.2855955862960.233894301757-0.07397382292220.5788907701380.1329083082760.04218359294660.3691222022130.04195395968240.48268333074931.2066648319-10.497001094234.1962592504
22.900295241830.253875988573-0.9316997006681.88967613463-0.1346745095894.03941607895-0.249725863979-0.187982029449-0.0141329014540.1712005370450.192211774119-0.18382125903-0.3738118256640.4897136899690.07388344876010.3510160333290.0776213226911-0.06933480078850.4970905600520.06308356572410.43057517705713.22821253111.922284339116.6876506639
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 233 - 601 / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain B and resseq 233:601)BA - B
22(chain A and resseq 233:601)AC - D

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