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- PDB-9gwf: Human PPAR-gamma ligand binding domain in complex with LW100 -

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Basic information

Entry
Database: PDB / ID: 9gwf
TitleHuman PPAR-gamma ligand binding domain in complex with LW100
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 / 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 / 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 / negative regulation of cardiac muscle hypertrophy in response to stress / lipoprotein transport / positive regulation of vascular associated smooth muscle cell apoptotic process / WW domain binding / positive regulation of fatty acid metabolic process / STAT family protein binding / response to lipid / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / negative regulation of SMAD protein signal transduction / lipid homeostasis / E-box binding / alpha-actinin binding / R-SMAD binding / negative regulation of vascular associated smooth muscle cell proliferation / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / white fat cell differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / positive regulation of cholesterol efflux / negative regulation of BMP signaling pathway / cell fate commitment / negative regulation of osteoblast differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cell maturation / negative regulation of MAPK cascade / intracellular receptor signaling pathway / hormone-mediated signaling pathway / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / response to nutrient / epithelial cell differentiation / regulation of cellular response to insulin stimulus / peptide binding / negative regulation of miRNA transcription / negative regulation of angiogenesis / placenta development / positive regulation of apoptotic signaling pathway / Regulation of PTEN gene transcription / transcription coregulator binding / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / mRNA transcription by RNA polymerase II / fatty acid metabolic process / negative regulation of transforming growth factor beta receptor signaling pathway / PPARA activates gene expression / regulation of circadian rhythm / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / lipid metabolic process / positive regulation of miRNA transcription / regulation of blood pressure / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / nuclear receptor activity / 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 / 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 / intracellular membrane-bounded organelle / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II
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: 2.4 Å
AuthorsOerlemans, G.J.M. / Koops, A.A. / Brunsveld, L.
Funding support1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)
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
DepositionSep 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,1064
Polymers62,8212
Non-polymers1,2852
Water19811
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: PPARg is known to form homodimers in this space group
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-10 kcal/mol
Surface area23640 Å2
Unit cell
Length a, b, c (Å)93.738, 61.709, 119.132
Angle α, β, γ (deg.)90.000, 101.600, 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 234 through 251 or (resid 252...
d_2ens_1(chain "B" and ((resid 234 through 235 and (name N...

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_11METMETLYSLYSAA234 - 2681 - 35
d_12LYSLYSTHRTHRAA272 - 48939 - 243
d_13HISHISASPASPAA494 - 503248 - 257
d_14100100100100AC601
d_21METMETILEILEBB234 - 2901 - 54
d_22GLUGLUASPASPBB304 - 50363 - 258
d_23100100100100BD601

NCS oper: (Code: givenMatrix: (0.0915179318139, 0.981370883462, 0.168925004806), (0.985155965011, -0.113967619469, 0.128370971471), (0.145231514351, 0.15466923031, -0.977233460558)Vector: 15. ...NCS oper: (Code: given
Matrix: (0.0915179318139, 0.981370883462, 0.168925004806), (0.985155965011, -0.113967619469, 0.128370971471), (0.145231514351, 0.15466923031, -0.977233460558)
Vector: 15.3873315741, -24.5995933934, 47.1566813774)

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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-A1IPT / 4-[5-chloranyl-1-[2-chloranyl-6-(trifluoromethyl)phenyl]carbonyl-indazol-3-yl]-3-[[3-(methylcarbamoyl)phenyl]methoxy]benzoic acid


Mass: 642.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H20Cl2F3N3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.8 Å3/Da / Density % sol: 56.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.9M-1.2M sodium citrate tribasic dihydrate, 0.1M sodium cacodylate pH 6.4-7.4
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: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 2.4→58.35 Å / Num. obs: 25802 / % possible obs: 98.2 % / Redundancy: 6.5 % / CC1/2: 0.603 / Net I/σ(I): 5
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 2687 / CC1/2: 0.358

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB-REDOrefinement
REFMACV5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→58.35 Å / SU ML: 0.3711 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.109
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 1324 5.14 %RANDOM
Rwork0.2165 24432 --
obs0.2184 25756 97.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.44 Å2
Refinement stepCycle: LAST / Resolution: 2.4→58.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3966 0 88 11 4065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834128
X-RAY DIFFRACTIONf_angle_d1.03155600
X-RAY DIFFRACTIONf_chiral_restr0.0497651
X-RAY DIFFRACTIONf_plane_restr0.012713
X-RAY DIFFRACTIONf_dihedral_angle_d9.1856572
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.16721453247 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50.32391530.30622662X-RAY DIFFRACTION97.64
2.5-2.610.3261610.30242664X-RAY DIFFRACTION96.95
2.61-2.750.33661390.27862672X-RAY DIFFRACTION96.8
2.75-2.920.32151370.27582694X-RAY DIFFRACTION97.15
2.92-3.140.29891330.26682733X-RAY DIFFRACTION98.05
3.14-3.460.32821400.24382702X-RAY DIFFRACTION98.07
3.46-3.960.25211610.1952724X-RAY DIFFRACTION98.43
3.96-4.990.19661460.16682756X-RAY DIFFRACTION98.81
4.99-58.350.19121540.17982825X-RAY DIFFRACTION98.58
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)
13.001696472610.572962955181-0.9645012534511.52065279960.2529702874084.47127286859-0.197436563587-0.163475510755-0.134464379960.0817734826220.177412273791-0.221767577464-0.2487960969750.6067106562510.0003149151043920.2857805379250.0834893536827-0.04026994894710.3752152599920.006484252697280.34280591198913.208399876711.858834737317.0756787963
22.198716666240.2174679846710.3997938390151.371655878750.2281811758713.56009377614-0.00409939027354-0.132683716363-0.09817455417520.164210622454-0.01487248065830.175611360479-0.2327678600910.1921153580010.006633713876350.4154459426280.1514853241470.02010306336760.2825376242540.02759597323650.35966067114431.4154281905-10.692502173234.528316556
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 234 - 601 / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain A and resseq 234:601)AA - B
22(chain B and resseq 234:601)BC - D

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