3KMG

The X-ray Crystal Structure of PPAR-gamma in Complex with an Indole Derivative Modulator, GSK538, and an SRC-1 Peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Synthesis and biological activities of novel indole derivatives as potent and selective PPAR-gamma modulators

Lamotte, Y.Martres, P.Faucher, N.Laroze, A.Grillot, D.Ancellin, N.Saintillan, Y.Beneton, V.Gampe, R.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, D
272Homo sapiensMutation(s): 0 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Steroid Receptor Coactivator-1
B, E
27N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
538
Query on 538

Download SDF File 
Download CCD File 
A, D
4'-[(2,3-dimethyl-5-{[(1S)-1-phenylpropyl]carbamoyl}-1H-indol-1-yl)methyl]biphenyl-2-carboxylic acid
C34 H32 N2 O3
GAGNYMUXGIUCTR-HKBQPEDESA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
B, E
NON-POLYMERH2 N

--

ACE
Query on ACE
B, E
NON-POLYMERC2 H4 O

--

External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
538EC50: 0.8 - 2 nM (100) BINDINGDB
538IC50: 3 - 8 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 83.335α = 90.00
b = 84.158β = 90.00
c = 96.425γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
JDirectordata collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-11-10 
  • Released Date: 2010-01-12 
  • Deposition Author(s): Gampe, R.

Revision History 

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description
  • Version 1.3: 2018-01-24
    Type: Database references