5ZXI

Co-crystal structure of an Inhibitor in complex with human PPARdelta LBD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Selective PPAR delta Modulators Improve Mitochondrial Function: Potential Treatment for Duchenne Muscular Dystrophy (DMD).

Lagu, B.Kluge, A.F.Tozzo, E.Fredenburg, R.Bell, E.L.Goddeeris, M.M.Dwyer, P.Basinski, A.Senaiar, R.S.Jaleel, M.Tiwari, N.K.Panigrahi, S.K.Krishnamurthy, N.R.Takahashi, T.Patane, M.A.

(2018) ACS Med Chem Lett 9: 935-940

  • DOI: 10.1021/acsmedchemlett.8b00287

  • PubMed Abstract: 
  • The X-ray structure of the previously reported PPARδ modulator <b>1 </b> bound to the ligand binding domain (LBD) revealed that the amide moiety in <b>1 </b> exists in the thermodynamically disfavored <i>cis </i>-amide orientation. Isosteric repla ...

    The X-ray structure of the previously reported PPARδ modulator 1 bound to the ligand binding domain (LBD) revealed that the amide moiety in 1 exists in the thermodynamically disfavored cis -amide orientation. Isosteric replacement of the cis -amide with five-membered heterocycles led to the identification of imidazole 17 (MA-0204), a potent, selective PPARδ modulator with good pharmacokinetic properties. MA-0204 was tested in vivo in mice and in vitro in patient-derived muscle myoblasts (from Duchenne Muscular Dystrophy (DMD) patients); 17 altered the expression of PPARδ target genes and improved fatty acid oxidation, which supports the therapeutic hypothesis for the study of MA-0204 in DMD patients.


    Organizational Affiliation

    Aurigene Discovery Technologies, Ltd., Bengaluru and Hyderabad, India.,Astellas Pharma., Tsukuba, Japan.,Mitobridge, Inc. (a wholly owned subsidiary of Astellas Pharma.), 1030 Massachusetts Avenue, Cambridge, Massachusetts 02138, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor delta
A, B
275Homo sapiensMutation(s): 0 
Gene Names: PPARD (NR1C2, PPARB)
Find proteins for Q03181 (Homo sapiens)
Go to Gene View: PPARD
Go to UniProtKB:  Q03181
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9LU
Query on 9LU

Download SDF File 
Download CCD File 
A, B
6-[2-({2-[4-(furan-2-yl)phenyl]-5-methyl-1H-imidazol-1-yl}methyl)phenoxy]hexanoic acid
C27 H28 N2 O4
PZVNGYWXLMIOJJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.795α = 90.00
b = 76.644β = 97.81
c = 96.663γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release