9PLK

Interaction of human CYP3A4 with the drug darifenacin

これはPDB形式変換不可エントリーです。

9PLK の概要

• エントリーDOI: 10.2210/pdb9plk/pdb
• 分子名称: Cytochrome P450 3A4, PROTOPORPHYRIN IX CONTAINING FE, GLYCEROL, ... (5 entities in total)
• 機能のキーワード: cytochrome p450, cyp3a4, substrate, drug, darifenacin, complex, oxidoreductase
• 由来する生物種: Homo sapiens (human)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 56892.94

構造登録者

Sevrioukova, I.F. (登録日: 2025-07-15, 公開日: 2025-09-17, 最終更新日: 2025-10-22)

主引用文献

Sevrioukova, I.F.
Interaction of cytochrome P450 3A4 with cannabinoids and the drug darifenacin.
J.Biol.Chem., 301:110709-110709, 2025

PubMed Abstract: Cytochrome P450 3A4 (CYP3A4) is an important drug-metabolizing enzyme whose substrate binding mechanism remains incompletely understood because of insufficient structural information. This study investigated how CYP3A4 interacts with cannabinoids, (-)-trans-Δ-tetrahydrocannabinol (THC), cannabidiol and cannabinol, and a muscarinic receptor blocker, darifenacin, using spectral, mutagenesis, and structural approaches. It was found that THC and cannabidiol act as type I ligands and induce a nearly complete high-spin transition in CYP3A4 (K of 1.9 μM and 3.6 μM, respectively), whereas cannabinol causes only negligible spectral changes. In the crystal structure, THC approaches the heme with the cyclohexenyl C7 and C8 atoms, the main sites of metabolism, without triggering any significant structural perturbations. Darifenacin is also a type I ligand but has two binding sites (K of 11 μM and 712 μM) and associates to the high-affinity site in the crystal structure, where it adopts an arched conformation, placing the dihydrobenzofuran moiety above the heme suitably for the ring opening and C7 hydroxylation, the main routes of metabolism. Polar interactions with S119 and R212 facilitate but are not essential for the THC binding, likely driven by hydrophobic interactions and steric complementarity with the active site. In contrast, H-bonding to S119 is critical for the complex formation with darifenacin. The new X-ray models have expanded the structural library of productive complexes of CYP3A4 and helped identify a mechanism through which local changes in the active site could transmit to the remote areas to further optimize substrate binding and promote metabolism.

PubMed: 40945735
DOI: 10.1016/j.jbc.2025.110709

実験手法

X-RAY DIFFRACTION (2.25 Å)