SMTL ID : 6oo9.1

Human CYP3A4 bound to a drug mibefradil

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

4 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: MWV.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.6: 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: MWV.7 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 HEM.11: 28 residues within 4Å: Chain C: 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: MWV.12 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:I.98, C:F.117, C:F.282, C:V.293, C:I.349, C:A.350, C:F.415, C:F.415, C:I.423, C:F.427 Hydrogen bonds: C:S.417 Water bridges: C:R.85, C:R.355 Salt bridges: C:R.85, C:R.85, C:R.110, C:R.355, C:R.420 Metal complexes: C:C.422 HEM.16: 28 residues within 4Å: Chain D: 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: MWV.17 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:I.98, D:F.117, D:F.282, D:V.293, D:I.349, D:A.350, D:F.415, D:F.415, D:I.423, D:F.427 Hydrogen bonds: D:S.417 Water bridges: D:R.85, D:R.355 Salt bridges: D:R.85, D:R.85, D:R.110, D:R.355, D:R.420 Metal complexes: D:C.422

4 x MWV: (1S,2S)-2-(2-{[3-(1H-benzimidazol-2-yl)propyl](methyl)amino}ethyl)-6-fluoro-1-(propan-2-yl)-1,2,3,4-tetrahydronaphthalen-2-yl methoxyacetate(Non-covalent)

MWV.2: 15 residues within 4Å: Chain A: F.37, S.99, R.192, F.193, F.195, I.281, F.284, A.285, T.289, I.349, A.350, M.351, R.352, E.354 Ligands: HEM.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.195, A:F.284, A:F.284, A:A.285, A:T.289 Hydrogen bonds: A:R.192 Salt bridges: A:R.192 pi-Stacking: A:F.37 MWV.7: 15 residues within 4Å: Chain B: F.37, S.99, R.192, F.193, F.195, I.281, F.284, A.285, T.289, I.349, A.350, M.351, R.352, E.354 Ligands: HEM.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.195, B:F.284, B:F.284, B:A.285, B:T.289 Hydrogen bonds: B:R.192 Salt bridges: B:R.192 pi-Stacking: B:F.37 MWV.12: 15 residues within 4Å: Chain C: F.37, S.99, R.192, F.193, F.195, I.281, F.284, A.285, T.289, I.349, A.350, M.351, R.352, E.354 Ligands: HEM.11 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.195, C:F.284, C:F.284, C:A.285, C:T.289 Hydrogen bonds: C:R.192 Salt bridges: C:R.192 pi-Stacking: C:F.37 MWV.17: 15 residues within 4Å: Chain D: F.37, S.99, R.192, F.193, F.195, I.281, F.284, A.285, T.289, I.349, A.350, M.351, R.352, E.354 Ligands: HEM.16 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.195, D:F.284, D:F.284, D:A.285, D:T.289 Hydrogen bonds: D:R.192 Salt bridges: D:R.192 pi-Stacking: D:F.37

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: G.416, S.417, N.421, M.425 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.417, A:N.421 Water bridges: A:G.418 EDO.4: 4 residues within 4Å: Chain A: F.183, S.232, R.235, M.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.232 EDO.8: 4 residues within 4Å: Chain B: G.416, S.417, N.421, M.425 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.417, B:N.421 Water bridges: B:G.418 EDO.9: 4 residues within 4Å: Chain B: F.183, S.232, R.235, M.236 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.232 EDO.13: 4 residues within 4Å: Chain C: G.416, S.417, N.421, M.425 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.417, C:N.421 Water bridges: C:G.418 EDO.14: 4 residues within 4Å: Chain C: F.183, S.232, R.235, M.236 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.232 EDO.18: 4 residues within 4Å: Chain D: G.416, S.417, N.421, M.425 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.417, D:N.421 Water bridges: D:G.418 EDO.19: 4 residues within 4Å: Chain D: F.183, S.232, R.235, M.236 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.232

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 4 residues within 4Å: Chain A: F.199, I.218, C.219 Chain C: I.218 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.199 DMS.10: 4 residues within 4Å: Chain B: F.199, I.218, C.219 Chain D: I.218 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:F.199 DMS.15: 4 residues within 4Å: Chain A: I.218 Chain C: F.199, I.218, C.219 1 PLIP interactions: 1 interactions with chain C pi-Cation interactions: C:F.199 DMS.20: 4 residues within 4Å: Chain B: I.218 Chain D: F.199, I.218, C.219 1 PLIP interactions: 1 interactions with chain D pi-Cation interactions: D:F.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sevrioukova, I.F., Structural Insights into the Interaction of Cytochrome P450 3A4 with Suicide Substrates: Mibefradil, Azamulin and 6',7'-Dihydroxybergamottin. Int J Mol Sci (2019)

Release Date

2019-09-11

Peptides

Cytochrome P450 3A4: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Cytochrome P450 3A4

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