9GX5 | pdb_00009gx5

Human PPAR-gamma ligand binding domain in complex with AKGO173

PDB DOI: https://doi.org/10.2210/pdb9GX5/pdb

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

Deposited: 2024-09-27 Released: 2025-10-08
Deposition Author(s): Koops, A.A., Oerlemans, G.J.M., Brunsveld, L.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.270 (Depositor), 0.281 (DCC)
R-Value Work:
0.223 (Depositor), 0.231 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 63.96 kDa
Atom Count: 4,111
Modeled Residue Count: 521
Deposited Residue Count: 550
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A [auth B], B [auth A]	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P37231
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IQJ Query on A1IQJ Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth B]	C [auth B], D [auth A]	4-[5-chloranyl-1-[[2-chloranyl-6-(trifluoromethyl)phenyl]methyl]indazol-3-yl]-3-phenylmethoxy-benzoic acid C₂₉ H₁₉ Cl₂ F₃ N₂ O₃ ZTLYNNOYNSOQHJ-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.270 (Depositor), 0.281 (DCC)
R-Value Work: 0.223 (Depositor), 0.231 (DCC)
R-Value Observed: 0.225 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.479	α = 90
b = 61.74	β = 101.83
c = 119.034	γ = 90

Software Package:

Software Name	Purpose
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
Coot	model building
PHENIX	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Oerlemans, G.J.M.

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

Revision History (Full details and data files)

Version 1.0: 2025-10-08
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.