9PLJ

Crystal structure of human CYP3A4 with substrate THC

Summary for 9PLJ

• Entry DOI: 10.2210/pdb9plj/pdb
• Descriptor: Cytochrome P450 3A4, PROTOPORPHYRIN IX CONTAINING FE, (6aR,10aR)-6,6,9-trimethyl-3-pentyl-6a,7,8,10a-tetrahydro-6H-benzo[c]chromen-1-ol, ... (4 entities in total)
• Functional Keywords: cytochrome p450, cyp3a4, substrate, cannabinoid, complex, oxidoreductase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 56688.76

Authors

Sevrioukova, I.F. (deposition date: 2025-07-15, release date: 2025-09-17, Last modification date: 2025-10-22)

Primary citation

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 due to insufficient structural information. This study investigated how CYP3A4 interacts with cannabinoids, (-)-trans-Δ-tetrahydrocannabinol (THC), cannabidiol (CBD) and cannabinol (CBN), and a muscarinic receptor blocker, darifenacin, using spectral, mutagenesis and structural approaches. It was found that THC and CBD 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 CBN 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

Experimental method

X-RAY DIFFRACTION (2.72 Å)