3GBK

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


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
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B
271Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37231
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2PQ
Query on 2PQ

Download Ideal Coordinates CCD File 
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 
IDSourceBinding 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 = 56.502α = 90
b = 88.892β = 91.06
c = 58.371γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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