3B1M

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report



Literature

Pharmacology and in Vitro Profiling of a Novel Peroxisome Proliferator-Activated Receptor gamma Ligand, Cerco-A

Wakabayashi, K.Hayashi, S.Matsui, Y.Matsumoto, T.Furukawa, A.Kuroha, M.Tanaka, N.Inaba, T.Kanda, S.Tanaka, J.Okuyama, R.Wakimoto, S.Ogata, T.Araki, K.Ohsumi, J.

(2011) Biol Pharm Bull 34: 1094-1104

  • DOI: 10.1248/bpb.34.1094
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Peroxisome proliferator-activated receptor γ (PPARγ; NR1C3) is known as a key regulator of adipocytogenesis and the molecular target of thiazolidinediones (TZDs), also known as antidiabetic agents. Despite the clinical benefits of TZDs, their use is ...

    Peroxisome proliferator-activated receptor γ (PPARγ; NR1C3) is known as a key regulator of adipocytogenesis and the molecular target of thiazolidinediones (TZDs), also known as antidiabetic agents. Despite the clinical benefits of TZDs, their use is often associated with adverse effects including peripheral edema, congestive heart failure, and weight gain. Here we report the identification and characterization of a non-thiazolidinedione PPARγ partial agonist, Cerco-A, which is a derivative of the natural product, (-)-cercosporamide. Cerco-A was found to be a binder of the PPARγ ligand-binding domain in a ligand competitive binding assay and showed a unique cofactor recruitment profile compared to rosiglitazone. A crystal structure analysis revealed that Cerco-A binds to PPARγ without direct hydrogen bonding to helix12. In PPARγ transcriptional activation assay and an adipocyte differentiation assay, Cerco-A was a potent partial agonist of PPARγ. After a 14-day oral administration, once per day of Cerco-A in Zucker diabetic fatty (ZDF) rats, an apparent decrease of plasma glucose and triglyceride was observed, as with pioglitazone. To evaluate drug safety, Cerco-A was administered for 13 days orally in non-diabetic Zucker fatty (ZF) rats. Each of the hemodilution parameters (hematocrit, red blood cells number, and hemoglobin), which are considered as undesirable effects of TZDs, was improved significantly compared to pioglitazone. While Cerco-A showed body weight gain, as with pioglitazone, Cerco-A had significantly lower effects on heart and white adipose tissues weight gain. The results suggest that Cerco-A offers beneficial effects on glycemic control with attenuated undesirable side effects.


    Organizational Affiliation

    Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305–8577, Japan. wakabayashi.kenji.vy@rda.daiichisankyo.co.jp



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A
283Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
Find proteins for P37231 (Homo sapiens)
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
B
19Homo sapiensMutation(s): 0 
Gene Names: PPARGC1ALEM6PGC1PGC1APPARGC1
Find proteins for Q9UBK2 (Homo sapiens)
Go to UniProtKB:  Q9UBK2
NIH Common Fund Data Resources
PHAROS  Q9UBK2
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KRC
Query on KRC

Download CCD File 
A
(9aS)-8-acetyl-N-[(2-ethylnaphthalen-1-yl)methyl]-1,7-dihydroxy-3-methoxy-9a-methyl-9-oxo-9,9a-dihydrodibenzo[b,d]furan-4-carboxamide
C30 H27 N O7
CCHJJXMWNNECOU-SSEXGKCCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KRCKi:  3.299999952316284   nM  Binding MOAD
KRCKi :  3.299999952316284   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.946α = 90
b = 54.622β = 92.21
c = 66.782γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-24
    Type: Initial release