3ET0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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

  • 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 ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gammaA, B292Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ET0 (Subject of Investigation/LOI)
Query on ET0

Download Ideal Coordinates CCD File 
C [auth A]3-(5-methoxy-1H-indol-3-yl)propanoic acid
C12 H13 N O3
ZLSZCJIWILJKMR-UHFFFAOYSA-N
 Ligand Interaction
GLC (Subject of Investigation/LOI)
Query on GLC

Download Ideal Coordinates CCD File 
D [auth B]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A, BL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing

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