3ET0 | pdb_00003et0

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 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3ET0

Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1073/pnas.0811325106
  • Primary Citation 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

Macromolecule Content 

  • Total Structure Weight: 67.15 kDa 
  • Atom Count: 4,289 
  • Modeled Residue Count: 519 
  • Deposited Residue Count: 584 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ET0

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
GLC

Query on GLC



Download:Ideal Coordinates CCD File
D [auth B]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CME
Query on CME
A, B
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.255 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
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

View Full Validation Report



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
  • Version 1.4: 2024-11-13
    Changes: Structure summary