Ligand binding domain of PPAR delta receptor in complex with a partial agonist

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Design of a partial PPARdelta agonist.

Pettersson, I.Ebdrup, S.Havranek, M.Pihera, P.Korinek, M.Mogensen, J.P.Jeppesen, C.B.Johansson, E.Sauerberg, P.

(2007) Bioorg Med Chem Lett 17: 4625-4629

  • DOI: https://doi.org/10.1016/j.bmcl.2007.05.079
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Structure based ligand design was used in order to design a partial agonist for the PPARdelta receptor. The maximum activation in the transactivation assay was reduced from 87% to 39%. The crystal structure of the ligand binding domain of the PPARdelta receptor in complex with compound 2 was determined in order to understand the structural changes which gave rise to the decrease in maximum activation.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor delta
A, B
283Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q03181 (Homo sapiens)
Explore Q03181 
Go to UniProtKB:  Q03181
PHAROS:  Q03181
GTEx:  ENSG00000112033 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03181
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1FA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C32 H27 F3 N2 O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
1FA BindingDB:  2Q5G EC50: 130 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.577α = 90
b = 65.603β = 124.05
c = 101.149γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PDB_EXTRACTdata extraction
d*TREKdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary