Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 34.67 kDa 
• Atom Count: 2448 
• Modelled Residue Count: 275 
• Deposited Residue Count: 298 
• Unique protein chains: 2

3LMP

Crystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative modulator

• PDB DOI: 10.2210/pdb3LMP/pdb

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


• Deposited: 2010-01-31 Released: 2010-04-14 
• Deposition Author(s): Matsui, Y., Hanzawa, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.242 
• R-Value Work: 0.203 
• R-Value Observed: 0.208 

Literature

Discovery of a novel selective PPARgamma modulator from (-)-Cercosporamide derivatives

Furukawa, A., Arita, T., Satoh, S., Wakabayashi, K., Hayashi, S., Matsui, Y., Araki, K., Kuroha, M., Ohsumi, J.

(2010) Bioorg Med Chem Lett 20: 2095-2098

• PubMed: 20219371 
• DOI: 10.1016/j.bmcl.2010.02.073
• Primary Citation of Related Structures:  
  3LMP


• PubMed Abstract: 
  

In an investigation of (-)-Cercosporamide derivatives with a plasma glucose-lowering effect, we found that N-benzylcarboxamide derivative 4 was a partial agonist of PPARgamma. A SAR study of the substituents on carboxamide nitrogen afforded the N-(1-naphthyl)methylcarboxamide derivative 23 as the most potent selective PPARgamma modulator. An X-ray crystallography study revealed that compound 23 bounded to the PPARgamma ligand binding domain in a unique way without any interaction with helix12. Compound 23 displayed a potent plasma glucose-lowering effect in db/db mice without the undesirable increase in body fluid and heart weight that is typically observed when PPARgamma full agonists are administrated.

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Organizational Affiliation: 

Shinagawa R&D Center, Daiichi Sankyo Co., Ltd, 1-2-58, Hiromachi, Shinagawa-ku, Tokyo, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A	283	Homo sapiens	Mutation(s): 0  Gene Names: NR1C3, PPARG
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
Peptide of Nuclear receptor coactivator 1	B [auth C]	15	N/A	Mutation(s): 0
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
CEK	C [auth A]	(9aS)-8-acetyl-1,7-dihydroxy-3-methoxy-9a-methyl-N-(1-naphthylmethyl)-9-oxo-9,9a-dihydrodibenzo[b,d]furan-4-carboxamide C28 H23 N O7 GHOGOLYMMHFNIT-MUUNZHRXSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CEK	Binding MOAD:  3LMP	Ki: 14 (nM) from 1 assay(s)
	PDBBind:  3LMP	IC50: 620 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.242 
• R-Value Work: 0.203 
• R-Value Observed: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.767	α = 90
b = 53.975	β = 92.37
c = 66.531	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
X-PLOR	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-01-31 
• Released Date: 2010-04-14 
Deposition Author(s): Matsui, Y., Hanzawa, H.

Revision History  

• Version 1.0: 2010-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description