2GTK

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

• PDB DOI: https://doi.org/10.2210/pdb2GTK/pdb

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


• Deposited: 2006-04-28 Released: 2006-09-26 
• Deposition Author(s): Kuhn, B., Hilpert, H., Benz, J., Binggeli, A., Grether, U., Humm, R., Maerki, H.-P., Meyer, M., Mohr, P.

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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 

Starting Model: other

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

• PubMed: 16737814 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

F. Hoffmann-La Roche Ltd, Discovery Research Basel, CH-4070 Basel, Switzerland. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.59 kDa 
• Atom Count: 2,434 
• Modelled Residue Count: 268 
• Deposited Residue Count: 281 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A	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 GTEx:  ENSG00000132170

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Decamer from Nuclear receptor coactivator 1	B	10	N/A	Mutation(s): 0  EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
208	C [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
208	BindingDB:  2GTK	IC50: 251 (nM) from 1 assay(s)
		EC50: 760 (nM) from 1 assay(s)
	PDBBind:  2GTK	IC50: 251 (nM) from 1 assay(s)

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 = 54.239	α = 90
b = 68.319	β = 90
c = 87.952	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-26 
Deposition Author(s): Kuhn, B., Hilpert, H., Benz, J., Binggeli, A., Grether, U., Humm, R., Maerki, H.-P., Meyer, M., Mohr, P.

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
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description