5YCN

Human PPARgamma ligand binding domain complexed with Lobeglitazone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for the Enhanced Anti-Diabetic Efficacy of Lobeglitazone on PPAR gamma.

Jang, J.Y.Bae, H.Lee, Y.J.Choi, Y.I.Kim, H.J.Park, S.B.Suh, S.W.Kim, S.W.Han, B.W.

(2018) Sci Rep 8: 31-31


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
Nuclear receptor coactivator 1
B
16Homo sapiensMutation(s): 0 
Gene Names: NCOA1 (BHLHE74, SRC1)
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to Gene View: NCOA1
Go to UniProtKB:  Q15788
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8LX
Query on 8LX

Download SDF File 
Download CCD File 
A
(5S)-5-[[4-[2-[[6-(4-methoxyphenoxy)pyrimidin-4-yl]-methyl-amino]ethoxy]phenyl]methyl]-1,3-thiazolidine-2,4-dione
Lobeglitazone
C24 H24 N4 O5 S
CHHXEZSCHQVSRE-FQEVSTJZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 130.959α = 90.00
b = 53.168β = 90.00
c = 54.856γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-09-07 
  • Released Date: 2018-09-12 
  • Deposition Author(s): Jang, J.Y., Han, B.W.

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2019-03-27
    Type: Data collection, Database references