6DH9

Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with MSDC-0602

• PDB DOI: https://doi.org/10.2210/pdb6DH9/pdb

• Classification: transcription/transcription inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-05-18 Released: 2019-05-22 
• Deposition Author(s): Shang, J., Kojetin, D.J.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.250 
• R-Value Work: 0.185 
• R-Value Observed: 0.191 

Starting Model: experimental

Literature

Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with MSDC-0602

Shang, J., Kojetin, D.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.52 kDa 
• Atom Count: 4,269 
• Modelled Residue Count: 515 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	271	Homo sapiens	Mutation(s): 0  Gene Names: PPARG, NR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
PHAROS:  P37231 GTEx:  ENSG00000132170

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GH1	C [auth A]	(5S)-5-({4-[2-(3-methoxyphenyl)-2-oxoethoxy]phenyl}methyl)-1,3-thiazolidine-2,4-dione C19 H17 N O5 S YAUMOGALQJYOJQ-KRWDZBQOSA-N
KNA	D [auth A]	nonanoic acid C9 H18 O2 FBUKVWPVBMHYJY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GH1	BindingDB:  6DH9	IC50: 1.81e+4 (nM) from 1 assay(s)
		EC50: 961 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.250 
• R-Value Work: 0.185 
• R-Value Observed: 0.191 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.12	α = 90
b = 60.2	β = 103.59
c = 118.04	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-22 
Deposition Author(s): Shang, J., Kojetin, D.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01DK101871

Revision History  

• Version 1.0: 2019-05-22
  Type: Initial release
  
• Version 1.1: 2019-12-25
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description