8YT9: Human PPAR alpha ligand binding domain

Human PPAR alpha ligand binding domain in complex with a 1H-pyrazolo[3,4-b]pyridine-derived compound. Determined by X-ray diffraction at 1.59 Å resolution. Released 2 Apr 2025.

Method: X-ray diffraction
Resolution: 1.59 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,333
Mol. weight: 33.62 kDa
Ligands: A1LZY
Released: 2 Apr 2025

Explore 8YT9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YT9 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 A: 17 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	203-217	15
α-helix	222-228	7
α-helix	238	1
β-strand	239-241	3	1
α-helix	244-254	11
α-helix	268-293	26
α-helix	297-299	3
α-helix	302-321	20
α-helix	322-324	3
β-strand	325-326	2	1
β-strand	329-332	4	1
β-strand	337-340	4	1
α-helix	341-346	6
α-helix	348	1
α-helix	351-353	3
α-helix	356-366	11
α-helix	372-383	12
α-helix	394-415	22
α-helix	422-450	29
α-helix	455-457	3
α-helix	458-464	7

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	143-149	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peroxisome proliferator-activated receptor alpha	A	protein	272	Homo sapiens	Q07869 (AlphaFold model)
Peroxisome proliferator-activated receptor gamma coactivator 1-alpha	B	protein	22	Homo sapiens	Q9UBK2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8YT9_1 Peroxisome proliferator-activated receptor alpha (chains A)
GGQTADLKSLAKRIYEAYLKNFNMNKVKARVILSGKASNNPPFVIHDMETLCMAEKTLVA
KLVANGIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEA
IFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDIS
LFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQL
VTEHAQLVQIIKKTESDAALHPLLQEIYRDMY

Sequence of entity 2 (B), FASTA

>8YT9_2 Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (chains B)
PQEAEEPSLLKKLLLAPANTQL

Ligands and cofactors

ID	Name	Formula	Copies
A1LZY	1-(4-fluorophenyl)-6-[2-(5-methyl-2-phenyl-1,3-oxazol-4-yl)ethoxy]-3-pentan-3-y…	C30 H29 F N4 O4	1

Primary citation

Structural evolution of 1H-pyrazolo[3,4-b]pyridine-derived PPARalpha activators as leads for nonalcoholic steatohepatitis. Tachibana, K., Morie, T., Fukuda, S. et al. To be published.

Other PDB entries of the same protein (UniProt Q07869 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KAX 1.23 Å, X-ray structure of human PPARalpha ligand binding domain-intrinsic fatty acid (E. coli…
6LXA 1.23 Å, X-ray structure of human PPARalpha ligand binding domain-eicosapentaenoic acid (EPA)…
6KB1 1.25 Å, X-ray structure of human PPARalpha ligand binding domain-tetradecylthioacetic acid (TTA)…
6LX6 1.3 Å, X-ray structure of human PPARalpha ligand binding domain-palmitic acid co-crystals…
6KB0 1.35 Å, X-ray structure of human PPARalpha ligand binding domain-5,8,11,14-eicosatetraynoic acid…
9IWM 1.39 Å, X-ray structure of human PPARalpha ligand binding domain-GW7647-TRAP220 coactivator…
6LX9 1.4 Å, X-ray structure of human PPARalpha ligand binding domain-arachidonic acid co-crystals…
6LX7 1.41 Å, X-ray structure of human PPARalpha ligand binding domain-stearic acid co-crystals…
6KB4 1.42 Å, X-ray structure of human PPARalpha ligand binding domain-pemafibrate co-crystals…
6KB6 1.43 Å, X-ray structure of human PPARalpha ligand binding domain-tetradecylthioacetic acid (TTA)…
6KB3 1.45 Å, X-ray structure of human PPARalpha ligand binding domain-GW7647 co-crystals obtained by…
9VZS 1.46 Å, X-ray structure of human PPARalpha ligand binding domain-10-hydroxystearic acid (10-HSA)…

Browse structure collections

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