SMTL ID : 6oob.1

Human CYP3A4 bound to a suicide substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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: MWS.2 19 PLIP interactions: 18 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:I.98, A:F.117, A:F.282, A:A.285, 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 Salt bridges: A:R.85, A:R.85, A:R.110, A:R.355, A:R.420 Metal complexes: A:C.422, H2O.1 HEM.3: 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: MWS.4 19 PLIP interactions: 18 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:I.98, B:F.117, B:F.282, B:A.285, 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 Salt bridges: B:R.85, B:R.85, B:R.110, B:R.355, B:R.420 Metal complexes: B:C.422, H2O.3 HEM.5: 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: MWS.6 19 PLIP interactions: 18 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:I.98, C:F.117, C:F.282, C:A.285, 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 Salt bridges: C:R.85, C:R.85, C:R.110, C:R.355, C:R.420 Metal complexes: C:C.422, H2O.4 HEM.7: 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: MWS.8 19 PLIP interactions: 18 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: D:I.98, D:F.117, D:F.282, D:A.285, 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 Salt bridges: D:R.85, D:R.85, D:R.110, D:R.355, D:R.420 Metal complexes: D:C.422, H2O.6

4 x MWS: 4-{[(2Z,6S)-6,7-dihydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-7H-furo[3,2-g][1]benzopyran-7-one(Non-covalent)

MWS.2: 15 residues within 4Å: Chain A: F.37, S.99, R.192, F.195, I.281, F.284, A.285, T.289, I.349, A.350, M.351, R.352, L.353, E.354 Ligands: HEM.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.37, A:F.37, A:F.195, A:A.285, A:A.350, A:M.351, A:E.354 Hydrogen bonds: A:S.99, A:E.354 Water bridges: A:R.352 pi-Cation interactions: A:R.192 MWS.4: 15 residues within 4Å: Chain B: F.37, S.99, R.192, F.195, I.281, F.284, A.285, T.289, I.349, A.350, M.351, R.352, L.353, E.354 Ligands: HEM.3 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.37, B:F.37, B:F.195, B:A.285, B:A.350, B:M.351, B:E.354 Hydrogen bonds: B:S.99, B:E.354 Water bridges: B:R.352 pi-Cation interactions: B:R.192 MWS.6: 15 residues within 4Å: Chain C: F.37, S.99, R.192, F.195, I.281, F.284, A.285, T.289, I.349, A.350, M.351, R.352, L.353, E.354 Ligands: HEM.5 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.37, C:F.37, C:F.195, C:A.285, C:A.350, C:M.351, C:E.354 Hydrogen bonds: C:S.99, C:E.354 Water bridges: C:R.352 pi-Cation interactions: C:R.192 MWS.8: 15 residues within 4Å: Chain D: F.37, S.99, R.192, F.195, I.281, F.284, A.285, T.289, I.349, A.350, M.351, R.352, L.353, E.354 Ligands: HEM.7 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.37, D:F.37, D:F.195, D:A.285, D:A.350, D:M.351, D:E.354 Hydrogen bonds: D:S.99, D:E.354 Water bridges: D:R.352 pi-Cation interactions: D:R.192

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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