5XMX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Novel highly selective peroxisome proliferator-activated receptor delta (PPAR delta) modulators with pharmacokinetic properties suitable for once-daily oral dosing.

Lagu, B.Kluge, A.F.Fredenburg, R.A.Tozzo, E.Senaiar, R.S.Jaleel, M.Panigrahi, S.K.Tiwari, N.K.Krishnamurthy, N.R.Takahashi, T.Patane, M.A.

(2017) Bioorg Med Chem Lett 27: 5230-5234

  • DOI: 10.1016/j.bmcl.2017.10.037
  • Primary Citation of Related Structures:  
    5XMX

  • PubMed Abstract: 
  • Optimization of benzamide PPARδ modulator 1 led to (E)-6-(2-((4-(furan-2-yl)-N-methylbenzamido)methyl)phenoxy)-4-methylhex-4-enoic acid (18), a potent selective PPARδ modulator with significantly improved exposure in multiple species following oral administration ...

    Optimization of benzamide PPARδ modulator 1 led to (E)-6-(2-((4-(furan-2-yl)-N-methylbenzamido)methyl)phenoxy)-4-methylhex-4-enoic acid (18), a potent selective PPARδ modulator with significantly improved exposure in multiple species following oral administration.


    Organizational Affiliation

    Mitobridge, Inc., 1030 Massachusetts Ave., Cambridge, MA 02138, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor deltaA, B275Homo sapiensMutation(s): 0 
Gene Names: PPARDNR1C2PPARB
UniProt & NIH Common Fund Data Resources
Find proteins for Q03181 (Homo sapiens)
Explore Q03181 
Go to UniProtKB:  Q03181
PHAROS:  Q03181
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
89L (Subject of Investigation/LOI)
Query on 89L

Download Ideal Coordinates CCD File 
C [auth A], D [auth B](E)-6-[2-[[[4-(furan-2-yl)phenyl]carbonyl-methyl-amino]methyl]phenoxy]-4-methyl-hex-4-enoic acid
C26 H27 N O5
WZFMWAHUFRLQRH-XDJHFCHBSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
89L BindingDB:  5XMX Kd: 57 (nM) from 1 assay(s)
EC50: min: 5, max: 270 (nM) from 7 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.84α = 90
b = 76.39β = 97.74
c = 96.73γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata processing
XDSdata reduction
XDSdata scaling
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release