2F4B

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Indol-1-yl Acetic Acids as Peroxisome Proliferator-Activated Receptor Agonists: Design, Synthesis, Structural Biology, and Molecular Docking Studies

Mahindroo, N.Wang, C.C.Liao, C.C.Huang, C.F.Lu, I.L.Lien, T.W.Peng, Y.H.Huang, W.J.Lin, Y.T.Hsu, M.C.Lin, C.H.Tsai, C.H.Hsu, J.T.Chen, X.Lyu, P.C.Chao, Y.S.Wu, S.Y.Hsieh, H.P.

(2006) J.Med.Chem. 49: 1212-1216

  • DOI: 10.1021/jm0510373

  • PubMed Abstract: 
  • A series of novel indole-based PPAR agonists is described leading to discovery of 10k, a highly potent PPAR pan-agonist. The structural biology and molecular docking studies revealed that the distances between the acidic group and the linker, when a ...

    A series of novel indole-based PPAR agonists is described leading to discovery of 10k, a highly potent PPAR pan-agonist. The structural biology and molecular docking studies revealed that the distances between the acidic group and the linker, when a ligand was complexed with PPARgamma protein, were important for the potent activity. The hydrophobic tail part of 10k makes intensive hydrophobic interaction with the PPARgamma protein resulting in potent activity.


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
271Homo sapiensMutation(s): 0 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EHA
Query on EHA

Download SDF File 
Download CCD File 
A
(5-{3-[(6-BENZOYL-1-PROPYL-2-NAPHTHYL)OXY]PROPOXY}-1H-INDOL-1-YL)ACETIC ACID
2-{5-[3-(6-BENZOYL-1-PROPYLNAPHTHALEN-2-YLOXY)PROPOXY]INDOL-1-YL}ETHANOIC ACID
C33 H31 N O5
ZXWVCCFKIRBLDP-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EHAIC50: 50 nM (100) BINDINGDB
EHAEC50: 70 nM (100) BINDINGDB
EHAIC50: 50 nM BINDINGMOAD
EHAIC50: 50 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.967α = 90.00
b = 88.642β = 90.01
c = 57.878γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
REFMACrefinement
HKL-2000data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance