6AD9

Crystal Structure of PPARgamma Ligand Binding Domain in complex with dibenzooxepine derivative compound-9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Development of Dihydrodibenzooxepine Peroxisome Proliferator-Activated Receptor (PPAR) Gamma Ligands of a Novel Binding Mode as Anticancer Agents: Effective Mimicry of Chiral Structures by Olefinic E/ Z-Isomers.

Yamamoto, K.Tamura, T.Henmi, K.Kuboyama, T.Yanagisawa, A.Matsubara, M.Takahashi, Y.Suzuki, M.Saito, J.I.Ueno, K.Shuto, S.

(2018) J. Med. Chem. 61: 10067-10083


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A
287Homo sapiensMutation(s): 0 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
12-mer peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
B
12Homo sapiensMutation(s): 0 
Gene Names: PPARGC1A (LEM6, PGC1, PGC1A, PPARGC1)
Find proteins for Q9UBK2 (Homo sapiens)
Go to Gene View: PPARGC1A
Go to UniProtKB:  Q9UBK2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KK4
Query on KK4

Download SDF File 
Download CCD File 
A
3-[(1E)-1-{8-[(4-methyl-2-propyl-1H-benzimidazol-1-yl)methyl]dibenzo[b,e]oxepin-11(6H)-ylidene}ethyl]-1,2,4-oxadiazol-5(4H)-one
C30 H28 N4 O3
KWALRLFFHWLMRU-ZXVVBBHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.730α = 90.00
b = 54.338β = 108.61
c = 66.770γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2018-12-05
    Type: Data collection, Database references