9GZ9 | pdb_00009gz9

Human PPAR-gamma ligand binding domain in complex with AKGO48

• PDB DOI: https://doi.org/10.2210/pdb9GZ9/pdb

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


• Deposited: 2024-10-03 Released: 2025-10-15 
• Deposition Author(s): Oerlemans, G.J.M., Koops, A.A., Brunsveld, L.
• Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.261 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Development and characterization of novel indazole-based PPAR-gamma partial agonists

Koops, A.A., Oerlemans, G.J.M., Brunsveld, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 64.13 kDa 
• Atom Count: 3,983 
• Modeled Residue Count: 516 
• Deposited Residue Count: 550 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	275	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IQ6 (Subject of Investigation/LOI)	C [auth A], D [auth B]	4-[5-chloranyl-1-[2-chloranyl-6-(trifluoromethyl)phenyl]carbonyl-indazol-3-yl]-3-[(3,4-dichlorophenyl)methoxy]benzoic acid C29 H15 Cl4 F3 N2 O4 UAPDXFTWMZWVRB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.261 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Diffraction Data: https://doi.org/10.15151/ESRF-ES-1119943221

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.335	α = 90
b = 61.706	β = 101.39
c = 118.573	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing
PDB-REDO	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Oerlemans, G.J.M., Koops, A.A., Brunsveld, L.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	--

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release