2Q5G

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1016/j.bmcl.2007.05.079
  • Primary Citation of Related Structures:  
    2Q5G

  • 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 ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor delta AB283Homo sapiensMutation(s): 0 
Gene Names: PPARDNR1C2PPARB
Find proteins for Q03181 (Homo sapiens)
Explore Q03181 
Go to UniProtKB:  Q03181
NIH Common Fund Data Resources
PHAROS:  Q03181
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1FA
Query on 1FA

Download Ideal Coordinates CCD File 
A, B
[(7-{[2-(3-MORPHOLIN-4-YLPROP-1-YN-1-YL)-6-{[4-(TRIFLUOROMETHYL)PHENYL]ETHYNYL}PYRIDIN-4-YL]THIO}-2,3-DIHYDRO-1H-INDEN- 4-YL)OXY]ACETIC ACID
C32 H27 F3 N2 O4 S
AKQAEZPFLKFQCZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1FAEC50:  130   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction
PHASESphasing

Structure Validation

View Full Validation Report



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