2ATH

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

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 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • 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 ...

    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.

    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
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator activated receptor gammaA, B271Homo sapiensMutation(s): 0 
Gene Names: PPARG, NR1C3
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231
GTEx  ENSG00000132170
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3EA
Query on 3EA
Download CCD File 
A, 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		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3EAIC50:  152.0500030517578   nM  BindingDB
3EAIC50:  152   nM  Binding MOAD
3EAIC50 :  152   nM  PDBBind
3EAIC50:  152   nM  BindingDB
3EAEC50:  230   nM  BindingDB
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 = 55.78α = 90
b = 88.523β = 90.43
c = 57.565γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

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