3D5F

Crystal Structure of PPAR-delta complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.278 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

PPAR-Delta Activation Contributes to Neuroprotectio Against Thapsigargin-Induced SH-SY5Y Cell Death

Iwashita, A.Mihara, K.Amano, Y.Orita, M.Matsuoka, N.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor deltaA, B267Homo sapiensMutation(s): 1 
Gene Names: PPARDNR1C2PPARB
UniProt & NIH Common Fund Data Resources
Find proteins for Q03181 (Homo sapiens)
Explore Q03181 
Go to UniProtKB:  Q03181
PHAROS:  Q03181
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03181
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L41
Query on L41

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
{4-[3-(4-acetyl-3-hydroxy-2-propylphenoxy)propoxy]phenoxy}acetic acid
C22 H26 O7
HBBVCKCCQCQCTJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
L41 BindingDB:  3D5F Kd: min: 0.43, max: 76 (nM) from 2 assay(s)
IC50: 13 (nM) from 1 assay(s)
EC50: min: 20, max: 3800 (nM) from 10 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.278 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.456α = 90
b = 92.829β = 98.02
c = 96.454γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2008-05-16 
  • Released Date: 2008-06-03 
  • Deposition Author(s): Amano, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations