2GTK

Structure-based Design of Indole Propionic Acids as Novel PPARag CO-Agonists

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structure-based design of indole propionic acids as novel PPARalpha/gamma co-agonists

Kuhn, B., Hilpert, H., Benz, J., Binggeli, A., Grether, U., Humm, R., Meyer, M., Mohr, P.

(2006) Bioorg Med Chem Lett 16: 4016-4020

  • DOI: 10.1016/j.bmcl.2006.05.007
  • Primary Citation of Related Structures:  
    2GTK

  • PubMed Abstract: 

    • In the quest for novel PPARalpha/gamma co-agonists as putative drugs for the treatment of type 2 diabetes and dyslipidemia, we have used a structure-based design approach to identify propionic acids with a 1,5-disubstituted indole scaffold as potent PPAR ...

    In the quest for novel PPARalpha/gamma co-agonists as putative drugs for the treatment of type 2 diabetes and dyslipidemia, we have used a structure-based design approach to identify propionic acids with a 1,5-disubstituted indole scaffold as potent PPARalpha/gamma activators. Compounds 13, 24, and 28 are examples of submicromolar dual agonists with different alpha/gamma EC50 ratios that are selective against the delta-isoform. Analysis of the X-ray complex structure of PPARgamma with the indole propionic acid 13 provides a rationalization for some of the observed SAR.

    Organizational Affiliation: 

    F. Hoffmann-La Roche Ltd, Discovery Research Basel, CH-4070 Basel, Switzerland. bernd.kuhn@roche.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma A271Homo 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
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Decamer from Nuclear receptor coactivator 1 B10N/AMutation(s): 0 
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS:  Q15788
GTEx:  ENSG00000084676
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
208
Query on 208
Download Ideal Coordinates CCD File 
A
(2S)-3-(1-{[2-(2-CHLOROPHENYL)-5-METHYL-1,3-OXAZOL-4-YL]METHYL}-1H-INDOL-5-YL)-2-ETHOXYPROPANOIC ACID
C24 H23 Cl N2 O4
PAWOPJKHTZCKMT-QFIPXVFZSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
208IC50 :  250.99998474121094   nM  PDBBind
208IC50:  251   nM  BindingDB
208IC50:  250.99998474121094   nM  Binding MOAD
208EC50:  760   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.239α = 90
b = 68.319β = 90
c = 87.952γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description