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- PDB-9gvs: Human PPAR-gamma ligand binding domain in complex with AK176_C -

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Basic information

Entry
Database: PDB / ID: 9gvs
TitleHuman PPAR-gamma ligand binding domain in complex with AK176_C
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 / negative regulation of cardiac muscle hypertrophy in response to stress / DNA binding domain binding / 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 / E-box binding / lipid homeostasis / 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 / cellular response to low-density lipoprotein particle stimulus / negative regulation of lipid storage / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / 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 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / 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: 2.1 Å
AuthorsKoops, A.A. / Oerlemans, G.J.M. / 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
DepositionSep 25, 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
B: Peroxisome proliferator-activated receptor gamma
A: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4403
Polymers62,8212
Non-polymers6191
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, NR's are known to form homodimers in crystallization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-8 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.329, 61.918, 118.960
Angle α, β, γ (deg.)90.000, 102.176, 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_21HISHISLYSLYSBA233 - 2913 - 61
d_22LYSLYSLYSLYSBA303 - 50273 - 272

NCS oper: (Code: givenMatrix: (0.094950162432555, 0.98037489865954, 0.17277015000376), (0.98398032964858, -0.1187349315457, 0.13298393472711), (0.15088796346527, 0.15737558295088, -0.9759435169989) ...NCS oper: (Code: given
Matrix: (0.094950162432555, 0.98037489865954, 0.17277015000376), (0.98398032964858, -0.1187349315457, 0.13298393472711), (0.15088796346527, 0.15737558295088, -0.9759435169989)
Vector: -27.322741942539, 21.699773471534, 54.030761486543)

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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-A1IPR / 4-[1-[2-chloranyl-6-(trifluoromethyl)phenyl]carbonyl-6-(trifluoromethyl)indazol-3-yl]-3-phenylmethoxy-benzoic acid


Mass: 618.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H17ClF6N2O4 / Feature type: SUBJECT OF INVESTIGATION
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: 2.67 Å3/Da / Density % sol: 54 %
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: 0.8731 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 6, 2024
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.1→30.96 Å / Num. obs: 38853 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 46.94 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.3
Reflection shellResolution: 2.1→2.16 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 3208 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5refinement
PHENIX1.21.2-5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30.96 Å / SU ML: 0.3345 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.7633
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2553 1977 5.09 %
Rwork0.225 36858 -
obs0.2265 38835 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.93 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 43 0 4121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084193
X-RAY DIFFRACTIONf_angle_d0.97145679
X-RAY DIFFRACTIONf_chiral_restr0.0519666
X-RAY DIFFRACTIONf_plane_restr0.0099723
X-RAY DIFFRACTIONf_dihedral_angle_d18.89481538
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.3254397399599 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.38821460.36462669X-RAY DIFFRACTION99.72
2.15-2.210.30071320.33032604X-RAY DIFFRACTION99.82
2.21-2.280.30471510.31342585X-RAY DIFFRACTION99.96
2.28-2.350.3411500.28482632X-RAY DIFFRACTION99.5
2.35-2.430.29321380.26322595X-RAY DIFFRACTION99.53
2.43-2.530.27241200.25192629X-RAY DIFFRACTION99.46
2.53-2.650.2971560.25782617X-RAY DIFFRACTION99.75
2.65-2.780.31251390.25382598X-RAY DIFFRACTION99.02
2.79-2.960.26551460.25652615X-RAY DIFFRACTION99.28
2.96-3.190.33451270.27182624X-RAY DIFFRACTION99.89
3.19-3.510.27461510.24582667X-RAY DIFFRACTION99.96
3.51-4.010.26141340.20052649X-RAY DIFFRACTION99.89
4.01-5.050.17111290.17432668X-RAY DIFFRACTION99.79
5.05-30.960.2221580.18812706X-RAY DIFFRACTION99.41
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)
11.90487076206240.099387038159667-0.202723492318941.6178386674280.18642226126792.42219580297250.085690447264677-0.25386942981544-0.0110600857758290.194573766531860.0101907879110710.02666936032503-0.043768738937740.279196788644520.00649348102480230.266208593512820.118947969387040.0182846185597630.21160047375430.0353990874775960.27242224530027-15.881313356785-10.5115570549934.34976020075
21.9397924071170.30924529726159-0.152906575786061.26244856799910.274901214780732.8908529165711-0.20424571887973-0.0514560929937190.0023736141645919-0.0402642578010770.26848490651256-0.13983740016768-0.295466000408560.231410854484880.00203931883228530.334600604555670.11609906876364-0.0165795275846550.372112036420760.0270713716080940.34476298100021-33.73966000616511.78296632799416.797648014903
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain B and resseq 233:601)BA - B233 - 6011
22(chain A and resseq 233:503)AC233 - 5031 - 262

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