SMTL ID : 8so2.1

Human CYP3A4 bound to a substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 28 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, F.427, A.428, M.432 Ligands: CFF.2 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:I.98, A:F.117, A:F.282, A:V.293, A:I.349, A:A.350, A:F.415, A:F.415, A:I.423, A:F.427 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.8: 28 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, F.427, A.428, M.432 Ligands: CFF.9 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:I.98, B:F.117, B:F.282, B:V.293, B:I.349, B:A.350, B:F.415, B:F.415, B:I.423, B:F.427 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

12 x CFF: CAFFEINE(Non-covalent)

CFF.2: 6 residues within 4Å: Chain A: R.85, S.99, A.285, A.350 Ligands: HEM.1, CFF.3 No protein-ligand interaction detected (PLIP) CFF.3: 7 residues within 4Å: Chain A: R.192, I.281, F.284, T.289, I.349 Ligands: CFF.2, CFF.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.192 CFF.4: 8 residues within 4Å: Chain A: F.88, R.192, F.193, F.195, F.284, L.462 Ligands: CFF.3, CFF.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.193 CFF.5: 8 residues within 4Å: Chain A: F.37, D.56, R.86, P.87, F.88, F.195, T.204 Ligands: CFF.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.204 Water bridges: A:R.86 pi-Stacking: A:F.195, A:F.195 pi-Cation interactions: A:R.86 CFF.6: 6 residues within 4Å: Chain A: D.197, F.199, F.200, C.219, V.220 Ligands: CFF.7 2 PLIP interactions: 2 interactions with chain A pi-Stacking: A:F.199, A:F.199 CFF.7: 4 residues within 4Å: Chain A: C.219, V.220, P.222 Ligands: CFF.6 No protein-ligand interaction detected (PLIP) CFF.9: 6 residues within 4Å: Chain B: R.85, S.99, A.285, A.350 Ligands: HEM.8, CFF.10 No protein-ligand interaction detected (PLIP) CFF.10: 7 residues within 4Å: Chain B: R.192, I.281, F.284, T.289, I.349 Ligands: CFF.9, CFF.11 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.192 CFF.11: 8 residues within 4Å: Chain B: F.88, R.192, F.193, F.195, F.284, L.462 Ligands: CFF.10, CFF.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.193 CFF.12: 8 residues within 4Å: Chain B: F.37, D.56, R.86, P.87, F.88, F.195, T.204 Ligands: CFF.11 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.86 pi-Stacking: B:F.195, B:F.195 pi-Cation interactions: B:R.86 CFF.13: 6 residues within 4Å: Chain B: D.197, F.199, F.200, C.219, V.220 Ligands: CFF.14 2 PLIP interactions: 2 interactions with chain B pi-Stacking: B:F.199, B:F.199 CFF.14: 4 residues within 4Å: Chain B: C.219, V.220, P.222 Ligands: CFF.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sevrioukova, I.F., Interaction of CYP3A4 with caffeine: First insights into multiple substrate binding. J.Biol.Chem. (2023)

Release Date

2023-08-02

Peptides

Cytochrome P450 3A4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytochrome P450 3A4

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