2HFP

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

• PDB DOI: https://doi.org/10.2210/pdb2HFP/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-06-25 Released: 2006-09-19 
• Deposition Author(s): Pokross, M.E., Evdokimov, A.G., Walter, R.L., Mekel, M.J., Hopkins, C.R.

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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 

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

• PubMed: 16919947 
• 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.

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Organizational Affiliation: 

Procter and Gamble Pharmaceuticals, Health Care Research Center, 8700 Mason-Montgomery Road, Mason OH 45040, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.03 kDa 
• Atom Count: 2,528 
• Modelled Residue Count: 289 
• Deposited Residue Count: 303 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A	282	Homo sapiens	Mutation(s): 0  Gene Names: PPARG, NR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
PHAROS:  P37231 GTEx:  ENSG00000132170

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SRC Peptide Fragment	B	21	N/A	Mutation(s): 0  EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NSI	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
ID	Source	Binding Affinity
NSI	BindingDB:  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 = 46.487	α = 90
b = 77.178	β = 90
c = 82.075	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-19 
Deposition Author(s): Pokross, M.E., Evdokimov, A.G., Walter, R.L., Mekel, M.J., Hopkins, C.R.

Revision History  

• 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