Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 62.95 kDa 
• Atom Count: 4547 
• Modelled Residue Count: 542 
• Deposited Residue Count: 542 
• Unique protein chains: 1

2ATH

Crystal structure of the ligand binding domain of human PPAR-gamma im complex with an agonist

• PDB DOI: 10.2210/pdb2ATH/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-08-25 Released: 2006-08-25 
• Deposition Author(s): Mahindroo, N., Huang, C.-F., Wu, S.-Y., Hsieh, H.-P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.288 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 

Literature

Novel indole-based peroxisome proliferator-activated receptor agonists: design, SAR, structural biology, and biological activities

Mahindroo, N., Huang, C.-F., Peng, Y.-H., Wang, C.-C., Liao, C.-C., Lien, T.-W., Chittimalla, S.K., Huang, W.-J., Chai, C.-H., Prakash, E., Chen, C.-P., Hsu, T.-A., Peng, C.-H., Lu, I.-L., Lee, L.-H., Chang, Y.-W., Chen, W.-C., Chou, Y.-C., Chen, C.-T., Goparaju, C.M.V., Chen, Y.-S., Lan, S.-J., Yu, M.-C., Chen, X., Chao, Y.-S., Wu, S.-Y., Hsieh, H.-P.

(2005) J Med Chem 48: 8194-8208

• PubMed: 16366601 
• DOI: 10.1021/jm0506930
• Primary Citation of Related Structures:  
  2ATH


• PubMed Abstract: 
  

The synthesis and structure-activity relationship studies of novel indole derivatives as peroxisome proliferator-activated receptor (PPAR) agonists are reported. Indole, a drug-like scaffold, was studied as a core skeleton for the acidic head part of PPAR agonists. The structural features (acidic head, substitution on indole, and linker) were optimized first, by keeping benzisoxazole as the tail part, based on binding and functional activity at PPARgamma protein. The variations in the tail part, by introducing various heteroaromatic ring systems, were then studied. In vitro evaluation led to identification of a novel series of indole compounds with a benzisoxazole tail as potent PPAR agonists with the lead compound 14 (BPR1H036) displaying an excellent pharmacokinetic profile in BALB/c mice and an efficacious glucose lowering activity in KKA(y) mice. Structural biology studies of 14 showed that the indole ring contributes strong hydrophobic interactions with PPARgamma and could be an important moiety for the binding to the protein.

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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, Republic of China.

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: PPARG, NR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
PHAROS:  P37231

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3EA	C [auth A], D [auth B]	2-{5-[3-(7-PROPYL-3-TRIFLUOROMETHYLBENZO[D]ISOXAZOL-6-YLOXY)PROPOXY]INDOL-1-YL}ETHANOIC ACID C24 H23 F3 N2 O5 TWVYNPULGKGJOS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3EA	BindingDB:  2ATH	IC50: min: 152, max: 152.05 (nM) from 2 assay(s)
		EC50: 230 (nM) from 1 assay(s)
	PDBBind:  2ATH	IC50: 152 (nM) from 1 assay(s)
	Binding MOAD:  2ATH	IC50: 152 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.288 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.78	α = 90
b = 88.523	β = 90.43
c = 57.565	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-08-25 
• Released Date: 2006-08-25 
Deposition Author(s): Mahindroo, N., Huang, C.-F., Wu, S.-Y., Hsieh, H.-P.

Revision History  

• Version 1.0: 2006-08-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance