6LXC

X-ray structure of human PPARalpha ligand binding domain-saroglitazar co-crystals obtained by delipidation and cross-seeding

Summary for 6LXC

• Entry DOI: 10.2210/pdb6lxc/pdb
• Descriptor: Peroxisome proliferator-activated receptor alpha, (2S)-2-ethoxy-3-[4-[2-[2-methyl-5-(4-methylsulfanylphenyl)pyrrol-1-yl]ethoxy]phenyl]propanoic acid (3 entities in total)
• Functional Keywords: nuclear receptor, protein-ligand complex, ppar, transcription
• Biological source: Homo sapiens
• Total number of polymer chains: 1
• Total formula weight: 31295.62

Authors

Kamata, S.,Honda, A.,Ishikawa, R.,Akahane, M.,Oyama, T.,Ishii, I. (deposition date: 2020-02-10, release date: 2020-11-11, Last modification date: 2023-11-29)

Primary citation

Kamata, S.,Oyama, T.,Saito, K.,Honda, A.,Yamamoto, Y.,Suda, K.,Ishikawa, R.,Itoh, T.,Watanabe, Y.,Shibata, T.,Uchida, K.,Suematsu, M.,Ishii, I.
PPAR alpha Ligand-Binding Domain Structures with Endogenous Fatty Acids and Fibrates.
Iscience, 23:101727-101727, 2020

PubMed Abstract: Most triacylglycerol-lowering fibrates have been developed in the 1960s-1980s before their molecular target, peroxisome proliferator-activated receptor alpha (PPARα), was identified. Twenty-one ligand-bound PPARα structures have been deposited in the Protein Data Bank since 2001; however, binding modes of fibrates and physiological ligands remain unknown. Here we show thirty-four X-ray crystallographic structures of the PPARα ligand-binding domain, which are composed of a "Center" and four "Arm" regions, in complexes with five endogenous fatty acids, six fibrates in clinical use, and six synthetic PPARα agonists. High-resolution structural analyses, in combination with coactivator recruitment and thermostability assays, demonstrate that stearic and palmitic acids are presumably physiological ligands; coordination to Arm III is important for high PPARα potency/selectivity of pemafibrate and GW7647; and agonistic activities of four fibrates are enhanced by the partial agonist GW9662. These results renew our understanding of PPARα ligand recognition and contribute to the molecular design of next-generation PPAR-targeted drugs.

PubMed: 33205029
DOI: 10.1016/j.isci.2020.101727

Experimental method

X-RAY DIFFRACTION (2.03 Å)