8AQM: PPARG and NCOR2 with an inverse agonist

Crystal structure of PPARG and NCOR2 with an inverse agonist (compound 6a). Determined by X-ray diffraction at 2.3 Å resolution. Released 9 Nov 2022.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,521
Mol. weight: 69.82 kDa
Ligands: O2O
Released: 9 Nov 2022

Explore 8AQM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8AQM contains 35 α-helices and 8 β-strands across 4 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 A: 16 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	206-225	20
α-helix	230-237	8
α-helix	246	1
β-strand	247-249	3	1
α-helix	252-258	7
α-helix	277-288	12
α-helix	290-301	12
α-helix	306-308	3
α-helix	311-332	22
β-strand	334	1	1
β-strand	338-341	4	1
β-strand	346-349	4	1
α-helix	350-355	6
α-helix	357	1
α-helix	360-362	3
α-helix	365-375	11
α-helix	381-392	12
α-helix	403-424	22
α-helix	431-456	26
α-helix	467-473	7

Chain B: 17 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	208-225	18
α-helix	230-237	8
α-helix	244-246	3
β-strand	247-249	3	2
α-helix	252-258	7
α-helix	259-261	3
α-helix	283-301	19
α-helix	311-332	22
β-strand	334-335	2	2
β-strand	338-341	4	2
α-helix	342-344	3
β-strand	346-349	4	2
α-helix	350-354	5
α-helix	357	1
α-helix	360-362	3
α-helix	365-375	11
α-helix	381-392	12
α-helix	403-424	22
α-helix	431-450	20
α-helix	453-457	5
α-helix	466-472	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2348-2358	11

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2350-2358	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peroxisome proliferator-activated receptor gamma	A, B	protein	279	Homo sapiens	P37231 (AlphaFold model)
Nuclear receptor corepressor 2	C, D	protein	23	Homo sapiens	Q9Y618 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8AQM_1 Peroxisome proliferator-activated receptor gamma (chains A, B)
GSHMQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMG
EDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLL
KYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALE
LDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQK
MTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY

Sequence of entity 2 (C, D), FASTA

>8AQM_2 Nuclear receptor corepressor 2 (chains C, D)
HASTNMGLEAIIRKALMGKYDQW

Ligands and cofactors

ID	Name	Formula	Copies
O2O	2-chloranyl-~{N}-[2-(3-methylphenyl)-1,3-benzoxazol-5-yl]-5-nitro-benzamide	C21 H14 Cl N3 O4	2

Primary citation

Discovery and Structure-Based Design of Potent Covalent PPAR gamma Inverse-Agonists BAY-4931 and BAY-0069 . Orsi, D.L., Pook, E., Brauer, N. et al. J Med Chem (2022) 65:14843-14863. DOI 10.1021/acs.jmedchem.2c01379 · 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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