3OZ0 | pdb_00003oz0

PPAR Delta in complex with azppard02

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.270 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3OZ0

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

Literature

Discovery of isoindoline and tetrahydroisoquinoline derivatives as potent, selective PPARδ agonists

Luckhurst, C.A., Stein, L.A., Furber, M., Webb, N., Ratcliffe, M.J., Allenby, G., Botterell, S., Tomlinson, W., Martin, B., Walding, A.

(2011) Bioorg Med Chem Lett 21: 492-496

  • DOI: https://doi.org/10.1016/j.bmcl.2010.10.117
  • Primary Citation Related Structures: 
    3OZ0

  • PubMed Abstract: 

    Small molecule isoindoline and tetrahydroisoquinoline derivatives have been identified as selective agonists of human peroxisome proliferator-activated receptor δ (PPARδ. Compound 18 demonstrated efficacy in a biomarker for increased fatty acid oxidation, with upregulation of pyruvate dehydrogenase kinase, isozyme 4 (PDK4) in human primary myotubes.

    • Organizational Affiliation: 
    • Medicinal Chemistry, AstraZeneca R&D Charnwood, Loughborough, Leicestershire LE11 5RH, UK. chris.luckhurst@astrazeneca.com

Macromolecule Content 

  • Total Structure Weight: 33.17 kDa 
  • Atom Count: 2,134 
  • Modeled Residue Count: 260 
  • Deposited Residue Count: 285 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor delta285Homo sapiensMutation(s): 0 
Gene Names: PPARD, NR1C2, PPARB
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
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3OZ

Query on 3OZ


Download:Ideal Coordinates CCD File
B [auth A][4-({(1S)-1-[(2,4-dichlorophenyl)carbamoyl]-1,3-dihydro-2H-isoindol-2-yl}methyl)-2-methylphenoxy]acetic acid
C25 H22 Cl2 N2 O4
MRCUMHGGUAFXSG-DEOSSOPVSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.270 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.258α = 90
b = 49.134β = 105.34
c = 58.574γ = 90
Software Package:
Software NamePurpose
RemDAqdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

  • Released Date: 2011-01-19 
    • Deposition Author(s): Ogg, D.

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-02-29
    Changes: Structure summary
  • Version 1.3: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 1.4: 2023-09-06
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description