3ET2

Structure of PPARdelta with 3-[5-Methoxy-1-(4-methoxy-benzenesulfonyl)-1H-indol-3-yl]-propionic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


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:  
    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 ...

    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 deltaAB287Homo sapiensMutation(s): 0 
Gene Names: PPARDNR1C2PPARB
Find proteins for Q03181 (Homo sapiens)
Explore Q03181 
Go to UniProtKB:  Q03181
NIH Common Fund Data Resources
PHAROS  Q03181
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ET1
Query on ET1

Download CCD File 
A, B
3-{5-methoxy-1-[(4-methoxyphenyl)sulfonyl]-1H-indol-3-yl}propanoic acid
C19 H19 N O6 S
YMPALHOKRBVHOJ-UHFFFAOYSA-N
 Ligand Interaction
1BO
Query on 1BO

Download CCD File 
A
1-BUTANOL
C4 H10 O
LRHPLDYGYMQRHN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.402α = 90
b = 94.353β = 98.27
c = 97.183γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
CCP4model building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Data collection