Structure of PPARgamma with 3-(5-Methoxy-1H-indol-3-yl)-propionic acid

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

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This is version 1.3 of the entry. See complete history


Scaffold-based discovery of indeglitazar, a PPAR pan-active anti-diabetic agent

Artis, D.R.Lin, J.J.Zhang, C.Wang, W.Mehra, U.Perreault, M.Erbe, D.Krupka, H.I.England, B.P.Arnold, J.Plotnikov, A.N.Marimuthu, A.Nguyen, H.Will, S.Signaevsky, M.Kral, J.Cantwell, J.Settachatgull, C.Yan, D.S.Fong, D.Oh, A.Shi, S.Womack, P.Powell, B.Habets, G.West, B.L.Zhang, K.Y.Milburn, M.V.Vlasuk, G.P.Hirth, K.P.Nolop, K.Bollag, G.Ibrahim, P.N.Tobin, J.F.

(2009) Proc Natl Acad Sci U S A 106: 262-267

  • DOI: https://doi.org/10.1073/pnas.0811325106
  • Primary Citation of Related Structures:  
    3ET0, 3ET1, 3ET2, 3ET3

  • PubMed Abstract: 

    In a search for more effective anti-diabetic treatment, we used a process coupling low-affinity biochemical screening with high-throughput co-crystallography in the design of a series of compounds that selectively modulate the activities of all three peroxisome proliferator-activated receptors (PPARs), PPARalpha, PPARgamma, and PPARdelta. Transcriptional transactivation assays were used to select compounds from this chemical series with a bias toward partial agonism toward PPARgamma, to circumvent the clinically observed side effects of full PPARgamma agonists. Co-crystallographic characterization of the lead molecule, indeglitazar, in complex with each of the 3 PPARs revealed the structural basis for its PPAR pan-activity and its partial agonistic response toward PPARgamma. Compared with full PPARgamma-agonists, indeglitazar is less potent in promoting adipocyte differentiation and only partially effective in stimulating adiponectin gene expression. Evaluation of the compound in vivo confirmed the reduced adiponectin response in animal models of obesity and diabetes while revealing strong beneficial effects on glucose, triglycerides, cholesterol, body weight, and other metabolic parameters. Indeglitazar has now progressed to Phase II clinical evaluations for Type 2 diabetes mellitus (T2DM).

  • Organizational Affiliation

    Plexxikon Inc., 91 Bolivar Drive, Berkeley, CA 94710, USA. drartis@plexxikon.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B
292Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ET0

Download Ideal Coordinates CCD File 
C [auth A]3-(5-methoxy-1H-indol-3-yl)propanoic acid
C12 H13 N O3
Query on GLC

Download Ideal Coordinates CCD File 
D [auth B]alpha-D-glucopyranose
C6 H12 O6
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CME
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.349α = 90
b = 62.451β = 101.73
c = 119.242γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
CCP4model building
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Refinement description, Structure summary