1ZEO

Crystal Structure of Human PPAR-gamma Ligand Binding Domain Complexed with an Alpha-Aryloxyphenylacetic Acid Agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Design and Synthesis of alpha-Aryloxyphenylacetic Acid Derivatives: A Novel Class of PPAR alpha/gamma Dual Agonists with Potent Antihyperglycemic and Lipid Modulating Activity

Shi, G.Q.Dropinski, J.F.McKeever, B.M.Xu, S.Becker, J.W.Berger, J.P.MacNaul, K.L.Elbrecht, A.Zhou, G.Doebber, T.W.Wang, P.Chao, Y.-S.Forrest, M.Heck, J.V.Moller, D.E.Jones, B.A.

(2005) J.Med.Chem. 48: 4457-4468

  • DOI: 10.1021/jm0502135

  • PubMed Abstract: 
  • The synthesis and structure-activity relationships of novel series of alpha-aryloxyphenylacetic acids as PPARalpha/gamma dual agonists are reported. The initial search for surrogates of the ester group in the screen lead led first to the optimization ...

    The synthesis and structure-activity relationships of novel series of alpha-aryloxyphenylacetic acids as PPARalpha/gamma dual agonists are reported. The initial search for surrogates of the ester group in the screen lead led first to the optimization of a subseries with a ketone moiety. Further efforts to modify the ketone subseries led to the design and synthesis of two new subseries containing fused heterocyclic ring systems. All these analogues were characterized by their "super" PPARalpha agonist activity and weak or partial agonist activity on PPARgamma in PPAR-GAL4 transactivation assays despite their similar binding affinities for both receptors. The cocrystal structures of compounds 7 and rosiglitazone with PPARgamma-LBD were compared, and significant differences were found in their interactions with the receptor. Select analogues in each subseries were further evaluated for in vivo efficacy. They all showed excellent anti-hyperglycemic efficacy in a db/db mouse model and hypolipidemic activity in hamster and dog models without provoking the typical PPARgamma-associated side effects in the rat tolerability assay.


    Organizational Affiliation

    Departments of Medicinal Chemistry, Merck Research Laboratories, P.O Box 2000, Rahway, New Jersey 07065-0900, USA. guoqiang_shi@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator activated receptor gamma
A, B
277Homo sapiensMutation(s): 0 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C01
Query on C01

Download SDF File 
Download CCD File 
A
(2S)-(4-ISOPROPYLPHENYL)[(2-METHYL-3-OXO-5,7-DIPROPYL-2,3-DIHYDRO-1,2-BENZISOXAZOL-6-YL)OXY]ACETATE
ALPHA-ARYLOXYPHENYLACETIC ACID AGONIST
C25 H30 N O5
RYNHNIDEKCRWHJ-QFIPXVFZSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C01IC50: 210 nM BINDINGMOAD
C01IC50: 210 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.219 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.573α = 90.00
b = 61.442β = 101.72
c = 118.051γ = 90.00
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data reduction
CNXphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-24
    Type: Database references