Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.59 kDa 
• Atom Count: 2283 
• Residue Count: 275 
• Unique protein chains: 2

6KTN

Human PPARgamma ligand-binding domain R288A mutant in complex with imatinib

• DOI: 10.2210/pdb6KTN/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-08-28 Released: 2020-02-05 
• Deposition Author(s): Jang, J.Y., Han, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.256 
• R-Value Work: 0.221 

Literature

Structural Basis for the Regulation of PPAR gamma Activity by Imatinib.

Jang, J.Y., Kim, H.J., Han, B.W.

(2019) Molecules 24

• PubMed: 31581474 
• DOI: 10.3390/molecules24193562
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Imatinib is an effective anticancer drug for the treatment of leukemia. Interestingly, when an FDA-approved drug library was tested for agents that block peroxisome proliferator-activated receptor γ (PPARγ) phosphorylation at Ser245 to evaluate possibilities of antidiabetic drug repositioning, imatinib was determined as a PPARγ antagonist ligand. However, it is not well understood how imatinib binds to PPARγ or would improve insulin sensitivity without classical agonism. Here, we report the crystal structure of the PPARγ R288A mutant in complex with imatinib. Imatinib bound to Arm2 and Arm3 regions in the ligand-binding domain (LBD) of PPARγ, of which the Arm3 region is closely related to the inhibition of PPARγ phosphorylation at Ser245. The binding of imatinib in LBD induced a stable conformation of helix H2' and the Ω loop compared with the ligand-free state. In contrast, imatinib does not interact with Tyr473 on PPARγ helix H12, which is important for the classical agonism associated with side effects. Our study provides new structural insights into the PPARγ regulation by imatinib and may contribute to the development of new antidiabetic drugs targeting PPARγ while minimizing known side effects.

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Organizational Affiliation: 

Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Peroxisome proliferator-activated receptor gamma	A	283	Homo sapiens	Mutation(s): 1  Gene Names: PPARG, NR1C3
Find proteins for P37231 (Homo sapiens) Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231 GTEx  ENSG00000132170

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
16-mer peptide from Nuclear receptor coactivator 1	B	16	Homo sapiens	Mutation(s): 0  Gene Names: NCOA1, BHLHE74, SRC1 EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens) Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS  Q15788 GTEx  ENSG00000084676

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STI	A	4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE C29 H31 N7 O KTUFNOKKBVMGRW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.256 
• R-Value Work: 0.221 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.928	α = 90
b = 52.779	β = 90
c = 53.438	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-08-28 
• Released Date: 2020-02-05 
Deposition Author(s): Jang, J.Y., Han, B.W.

Revision History 

• Version 1.0: 2020-02-05
  Type: Initial release