1NYX

Ligand binding domain of the human peroxisome proliferator activated receptor gamma in complex with an agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Synthesis and biological and structural characterization of the dual-acting peroxisome proliferator-activated receptor alpha/gamma agonist ragaglitazar

Ebdrup, S.Pettersson, I.Rasmussen, H.B.Deussen, H.-J.Frost Jensen, A.Mortensen, S.B.Fleckner, J.Pridal, L.Nygaard, L.Sauerberg, P.

(2003) J.MED.CHEM. 46: 1306-1317

  • DOI: 10.1021/jm021027r

  • PubMed Abstract: 
  • A new and improved synthesis of the peroxisome proliferator-activated receptor (PPAR) agonist ragaglitazar applicable for large-scale preparation has been developed. The convergent synthetic procedure was based on a novel enzymatic kinetic resolution ...

    A new and improved synthesis of the peroxisome proliferator-activated receptor (PPAR) agonist ragaglitazar applicable for large-scale preparation has been developed. The convergent synthetic procedure was based on a novel enzymatic kinetic resolution step. The conformation of ragaglitazar bound to the hPPARgamma receptor was quite different compared to the single-crystal structures of the l-arginine salt of ragaglitazar. In particular, the phenoxazine ring system had varying orientations. Ragaglitazar had high affinity for the hPPARalpha and -gamma receptors with IC(50) values of 0.98 and 0.092 microM, respectively. The lack of hPPARdelta activity could be explained by the absence of binding in the tail-up pocket in the hPPARdelta receptor, in contrast to the hPPARdelta agonist GW2433, which was able to bind in both the tail-up and tail-down pockets of the receptor.


    Organizational Affiliation

    Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark. sebd@novonordisk.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
peroxisome proliferator activated receptor gamma
A, B
276Homo sapiensGene 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
DRF
Query on DRF

Download SDF File 
Download CCD File 
A
(2S)-2-ETHOXY-3-{4-[2-(10H-PHENOXAZIN-10-YL)ETHOXY]PHENYL}PROPANOIC ACID
RAGAGLITAZAR
C25 H25 N O5
WMUIIGVAWPWQAW-DEOSSOPVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DRFEC50: 570 - 600 nM (100) BINDINGDB
DRFKi: 90 nM (100) BINDINGDB
DRFIC50: 92 nM (100) BINDINGDB
DRFIC50: 92 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.237 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 91.546α = 90.00
b = 62.090β = 102.91
c = 117.741γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNXrefinement
X-PLORphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-15
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance