2HFP

Crystal Structure of PPAR Gamma with N-sulfonyl-2-indole carboxamide ligands


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Design and synthesis of novel N-sulfonyl-2-indole carboxamides as potent PPAR-gamma binding agents with potential application to the treatment of osteoporosis.

Hopkins, C.R.O'neil, S.V.Laufersweiler, M.C.Wang, Y.Pokross, M.Mekel, M.Evdokimov, A.Walter, R.Kontoyianni, M.Petrey, M.E.Sabatakos, G.Roesgen, J.T.Richardson, E.Demuth Jr., T.P.

(2006) Bioorg Med Chem Lett 16: 5659-5663

  • DOI: https://doi.org/10.1016/j.bmcl.2006.08.003
  • Primary Citation of Related Structures:  
    2HFP

  • PubMed Abstract: 

    The synthesis and structure-activity relationships of a novel series of N-sulfonyl-2-indole carboxamides that bind to peroxisome proliferator-activated receptor gamma (PPAR-gamma) are reported. Chemical optimization of the series led to the identification of 4q (IC(50)=50 nM) as a potent binding agent of PPAR-gamma. Also reported is preliminary cell based data suggesting the use of these compounds in the treatment of osteoporosis.


  • Organizational Affiliation

    Procter and Gamble Pharmaceuticals, Health Care Research Center, 8700 Mason-Montgomery Road, Mason OH 45040, USA. Corey.Hopkins@sanofi-aventis.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma282Homo 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:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SRC Peptide Fragment21N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
GTEx:  ENSG00000084676 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15788
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NSI
Query on NSI

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
3-(4-METHOXYPHENYL)-N-(PHENYLSULFONYL)-1-[3-(TRIFLUOROMETHYL)BENZYL]-1H-INDOLE-2-CARBOXAMIDE
C30 H23 F3 N2 O4 S
BCPFCXDCWUXOGT-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NSI BindingDB:  2HFP IC50: 3 (nM) from 1 assay(s)
Binding MOAD:  2HFP IC50: 3 (nM) from 1 assay(s)
PDBBind:  2HFP IC50: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.487α = 90
b = 77.178β = 90
c = 82.075γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations