5Z5S

Crystal structure of the PPARgamma-LBD complexed with compound 13ab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of DS-6930, a potent selective PPAR gamma modulator. Part I: Lead identification.

Shinozuka, T.Tsukada, T.Fujii, K.Tokumaru, E.Shimada, K.Onishi, Y.Matsui, Y.Wakimoto, S.Kuroha, M.Ogata, T.Araki, K.Ohsumi, J.Sawamura, R.Watanabe, N.Yamamoto, H.Fujimoto, K.Tani, Y.Mori, M.Tanaka, J.

(2018) Bioorg. Med. Chem. 26: 5079-5098


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A
283Homo 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
Peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
C
19Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
RTE
Query on RTE

Download SDF File 
Download CCD File 
A
3-{[6-(4-chloro-3-fluorophenoxy)-1-methyl-1H-benzimidazol-2-yl]methoxy}benzoic acid
4-[[6-(4-chloro-3-fluoro-phenoxy)-1-methyl-benzimidazol-2-yl]methoxy]benzoic acid
C22 H16 Cl F N2 O4
QCDBYUFGXWPSLV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.408α = 90.00
b = 54.015β = 106.48
c = 66.242γ = 90.00
Software Package:
Software NamePurpose
CNXphasing
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Database references