SMTL ID : 9plk.1

Interaction of human CYP3A4 with the drug darifenacin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 27 residues within 4Å: Chain A: R.85, I.98, S.99, W.106, R.110, F.117, F.282, A.285, G.286, T.289, V.293, I.349, A.350, L.353, R.355, P.414, F.415, G.416, S.417, R.420, N.421, C.422, I.423, G.424, A.428, M.432 Ligands: 01.3 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:I.98, A:F.117, A:F.282, A:A.285, A:V.293, A:I.349, A:A.350, A:L.353, A:F.415, A:F.415, A:I.423 Hydrogen bonds: A:S.417 Water bridges: A:R.85, A:R.355 Salt bridges: A:R.85, A:R.85, A:R.110, A:R.355, A:R.420 Metal complexes: A:C.422 HEM.4: 27 residues within 4Å: Chain B: R.85, I.98, S.99, W.106, R.110, F.117, F.282, A.285, G.286, T.289, V.293, I.349, A.350, L.353, R.355, P.414, F.415, G.416, S.417, R.420, N.421, C.422, I.423, G.424, A.428, M.432 Ligands: 01.6 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:I.98, B:F.117, B:F.282, B:A.285, B:V.293, B:I.349, B:A.350, B:L.353, B:F.415, B:F.415, B:I.423 Hydrogen bonds: B:S.417 Water bridges: B:R.85, B:R.355 Salt bridges: B:R.85, B:R.85, B:R.110, B:R.355, B:R.420 Metal complexes: B:C.422

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: G.36, F.37, C.38, M.351, L.457, S.458, L.459, G.460, L.463 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.37, A:C.38, A:G.460 Water bridges: A:G.36, A:M.39 GOL.5: 9 residues within 4Å: Chain B: G.36, F.37, C.38, M.351, L.457, S.458, L.459, G.460, L.463 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.37, B:C.38, B:G.460 Water bridges: B:G.36, B:M.39

2 x 01: darifenacin

01.3: 10 residues within 4Å: Chain A: R.85, F.88, S.99, I.100, I.281, F.284, A.350, G.461, L.462 Ligands: HEM.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.88, A:F.88, A:I.281, A:F.284, A:L.462 Hydrogen bonds: A:S.99 pi-Cation interactions: A:R.85 01.6: 10 residues within 4Å: Chain B: R.85, F.88, S.99, I.100, I.281, F.284, A.350, G.461, L.462 Ligands: HEM.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.88, B:F.88, B:I.281, B:F.284, B:L.462 Hydrogen bonds: B:S.99 pi-Cation interactions: B:R.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sevrioukova, I.F., Interaction of cytochrome P450 3A4 with cannabinoids and the drug darifenacin. To Be Published

Release Date

2025-09-17

Peptides

Cytochrome P450 3A4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytochrome P450 3A4

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