3GBK

Crystal Structure of Human PPAR-gamma Ligand Binding Domain Complexed with a Potent and Selective Agonist

• PDB DOI: https://doi.org/10.2210/pdb3GBK/pdb

• Classification: ligand binding protein
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-02-19 Released: 2009-12-29 
• Deposition Author(s): Peng, Y.-H., Lin, C.-H., Hsieh, H.-P., Wu, S.-Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.298 
• R-Value Work: 0.230 
• R-Value Observed: 0.234 

Starting Model: experimental

Literature

Design and structural analysis of novel pharmacophores for potent and selective peroxisome proliferator-activated receptor gamma agonists

Lin, C.-H., Peng, Y.-H., Coumar, M.S., Chittimalla, S.K., Liao, C.-C., Lyn, P.-C., Huang, C.-C., Lien, T.-W., Lin, W.-H., Hsu, J.T.-A., Cheng, J.-H., Chen, X., Wu, J.-S., Chao, Y.-S., Lee, H.-J., Juo, C.-G., Wu, S.-Y., Hsieh, H.-P.

(2009) J Med Chem 52: 2618-2622

• PubMed: 19301897 
• DOI: https://doi.org/10.1021/jm801594x
• Primary Citation of Related Structures:  
  3GBK


• PubMed Abstract: 
  

  Utilizing medicinal chemistry design strategies such as benzo splitting and ring expansion, we converted PPARalpha/gamma dual agonist 1 to selective PPARgamma agonists 19 and 20. Compounds 19 and 20 were 2- to 4-fold better than rosiglitazone at PPARgamma receptor, with 80- to 100-fold PPARgamma selectivity over PPARalpha receptor. X-ray cocrystal studies in PPARgamma and modeling studies in PPARalpha give molecular insights for the improved PPARgamma potency and selectivity for 19 when compared to 1.

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Organizational Affiliation: 

Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 62.59 kDa 
• Atom Count: 4,473 
• Modelled Residue Count: 542 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	271	Homo sapiens	Mutation(s): 0  Gene Names: PPAR gamma
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
PHAROS:  P37231 GTEx:  ENSG00000132170

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PQ	C [auth A]	2-[(1-{3-[4-(biphenyl-4-ylcarbonyl)-2-propylphenoxy]propyl}-1,2,3,4-tetrahydroquinolin-5-yl)oxy]-2-methylpropanoic acid C38 H41 N O5 JWJGBYOYIUOQEB-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2PQ	BindingDB:  3GBK	EC50: 50 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.298 
• R-Value Work: 0.230 
• R-Value Observed: 0.234 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.502	α = 90
b = 88.892	β = 91.06
c = 58.371	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-29 
Deposition Author(s): Peng, Y.-H., Lin, C.-H., Hsieh, H.-P., Wu, S.-Y.

Revision History  

• Version 1.0: 2009-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description