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: 2.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gammaA,
C [auth D]
272Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
PHAROS:  P37231
GTEx:  ENSG00000132170 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37231
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Steroid Receptor Coactivator-1B,
D [auth E]
27N/AMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
538
Query on 538

Download Ideal Coordinates CCD File 
E [auth A],
F [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
538 BindingDB:  3KMG IC50: min: 0.37, max: 8 (nM) from 3 assay(s)
EC50: min: 0.8, max: 53 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.335α = 90
b = 84.158β = 90
c = 96.425γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
JDirectordata collection
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2018-01-24
    Changes: Database references
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-03-13
    Changes: Source and taxonomy, Structure summary