4R06

Crystal Structure of SR2067 bound to PPARgamma


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

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This is version 1.0 of the entry. See complete history


Literature

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: 10.1021/acschembio.5b00580
  • Primary Citation of Related Structures:  
    4R06

  • 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 ...

    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

    School of Biological Sciences, The University of Adelaide , Adelaide, South Australia 5005, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gammaA, B273Homo sapiensMutation(s): 0 
Gene Names: NR1C3PPARGPPARG_HUMAN
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
PHAROS:  P37231
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3E7 (Subject of Investigation/LOI)
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
SEVOIRSEDVSYGP-VWLOTQADSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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

  • Method: X-RAY DIFFRACTION
  • 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
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
MOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release