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

Experimental Data Snapshot

  • Resolution: 2.65 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1021/jm021027r
  • Primary Citation of Related Structures:  

  • 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 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
peroxisome proliferator activated receptor gamma
A, B
276Homo sapiensMutation(s): 0 
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DRF

Download Ideal Coordinates CCD File 
C25 H25 N O5
Binding Affinity Annotations 
IDSourceBinding Affinity
DRF BindingDB:  1NYX Ki: 90 (nM) from 1 assay(s)
IC50: 92 (nM) from 1 assay(s)
EC50: min: 570, max: 600 (nM) from 3 assay(s)
PDBBind:  1NYX IC50: 92 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.65 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.546α = 90
b = 62.09β = 102.91
c = 117.741γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-15
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations