9O9N: PPARgamma ligand binding domain

Crystal structure of PPARgamma ligand binding domain (LBD) in complex with NCoR1 corepressor peptide and inverse agonist FX-909. Determined by X-ray diffraction at 2.1 Å resolution. Released 14 May 2025.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,250
Mol. weight: 34.38 kDa
Ligands: A1CAA
Released: 14 May 2025

Explore 9O9N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9O9N contains 18 α-helices and 4 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain B: 17 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	206-225	20
α-helix	230-237	8
α-helix	245-246	2
β-strand	247-249	3	1
α-helix	252-257	6
α-helix	258-260	3
α-helix	277-287	11
α-helix	290-301	12
α-helix	311-332	22
β-strand	334-335	2	1
β-strand	338-341	4	1
α-helix	342-344	3
β-strand	346-349	4	1
α-helix	350-355	6
α-helix	357	1
α-helix	360-362	3
α-helix	365-376	12
α-helix	381-392	12
α-helix	403-424	22
α-helix	431-458	28
α-helix	467-474	8

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2261-2270	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peroxisome proliferator-activated receptor gamma	B	protein	276	Homo sapiens	P37231 (AlphaFold model)
Nuclear receptor corepressor 1	D	protein	23	Homo sapiens	O75376 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9O9N_1 Peroxisome proliferator-activated receptor gamma (chains B)
GQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDK
IKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYG
VHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDD
SDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTD
LRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY

Sequence of entity 2 (D), FASTA

>9O9N_2 Nuclear receptor corepressor 1 (chains D)
DPASNLGLEDIIRKALMGSFDDK

Ligands and cofactors

ID	Name	Formula	Copies
A1CAA	(3P)-3-(5,7-difluoro-4-oxo-1,4-dihydroquinolin-2-yl)-4-(methanesulfonyl)benzoni…	C17 H10 F2 N2 O3 S	1

Primary citation

Structural Basis of PPAR gamma-Mediated Transcriptional Repression by the Covalent Inverse Agonist FX-909. Laughlin, Z.T., Arifova, L., Munoz-Tello, P. et al. J Med Chem (2025) 68:17587-17597. DOI 10.1021/acs.jmedchem.5c01252 · PubMed

Other PDB entries of the same protein (UniProt P37231 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9F7W 1.25 Å, Human PPARgamma ligand binding domain in complex with co-activator 1alpha peptide and…
8BF1 1.36 Å, High-resolution structure of unliganded PPAR gamma in complex with the peptide PGC-1 alpha
9V8G 1.39 Å, PPARgamma ligand-binding domain in complex with PG08-NL
9V8H 1.39 Å, PPARgamma ligand-binding domain in complex with PG08-NL and rosiglitazone
8FKC 1.42 Å, Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and…
6MS7 1.43 Å, Peroxisome proliferator-activated receptor gamma ligand binding domain in complex with a…
9V8D 1.44 Å, PPARgamma ligand-binding domain in complex with PG08
3U9Q 1.52 Å, Ligand binding domain of PPARgamma complexed with Decanoic Acid and PGC-1a peptide
8B94 1.55 Å, Crystal structure of PPARG and NCOR2 with BAY-5516, an inverse agonist
8DKV 1.59 Å, PPARg bound to JTP-426467 and Co-R peptide
3B1M 1.6 Å, Crystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative…
3V9V 1.6 Å, Crystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative…

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