Crystal Structure of SR2067 bound to PPARgamma

Experimental Data Snapshot

  • Resolution: 2.22 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report

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SR2067 Reveals a Unique Kinetic and Structural Signature for PPAR gamma Partial Agonism.

van Marrewijk, L.M.Polyak, S.W.Hijnen, M.Kuruvilla, D.Chang, M.R.Shin, Y.Kamenecka, T.M.Griffin, P.R.Bruning, J.B.

(2016) ACS Chem Biol 11: 273-283

  • DOI: https://doi.org/10.1021/acschembio.5b00580
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Synthetic full agonists of PPARγ have been prescribed for the treatment of diabetes due to their ability to regulate glucose homeostasis and insulin sensitization. While the use of full agonists of PPARγ has been hampered due to severe side effects, partial agonists have shown promise due to their decreased incidence of such side effects in preclinical models. No kinetic information has been forthcoming in regard to the mechanism of full versus partial agonism of PPARγ to date. Here, we describe the discovery of a partial agonist, SR2067. A co-crystal structure obtained at 2.2 Å resolution demonstrates that interactions with the β-sheet are driven exclusively via hydrophobic interactions mediated through a naphthalene group, an observation that is unique from other partial agonists. Surface plasmon resonance revealed that SR2067 binds to the receptor with higher affinity (KD = 513 nM) as compared to that of full agonist rosiglitazone, yet it has a much slower off rate compared to that of rosiglitazone.

  • Organizational Affiliation

    GE Healthcare Life Sciences ANZ , Melbourne, Victoria 3121, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B
273Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
PHAROS:  P37231
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37231
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 3E7

Download Ideal Coordinates CCD File 
C [auth A]1-(naphthalen-1-ylsulfonyl)-N-[(1S)-1-phenylpropyl]-1H-indole-5-carboxamide
C28 H24 N2 O3 S
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
3E7 Binding MOAD:  4R06 Kd: 565 (nM) from 1 assay(s)
BindingDB:  4R06 IC50: 7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.22 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.79α = 90
b = 62.6β = 101.93
c = 118.57γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description