SMTL ID : 6ooa.1

Human CYP3A4 bound to a drug substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 26 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, 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: MWY.3 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:I.98, A:F.117, A:F.282, A:A.285, A:T.289, A:I.349, A:A.350, A:L.353, A:F.415, A:I.423, A:A.428 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 HEM.4: 26 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, 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: MWY.6 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:I.98, B:F.117, B:F.282, B:A.285, B:T.289, B:I.349, B:A.350, B:L.353, B:F.415, B:I.423, B:A.428 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 HEM.7: 26 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, 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: MWY.9 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:I.98, C:F.117, C:F.282, C:A.285, C:T.289, C:I.349, C:A.350, C:L.353, C:F.415, C:I.423, C:A.428 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 HEM.10: 26 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, 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: MWY.12 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:I.98, D:F.117, D:F.282, D:A.285, D:T.289, D:I.349, D:A.350, D:L.353, D:F.415, D:I.423, D:A.428 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

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 12 residues within 4Å: Chain A: K.35, G.36, F.37, C.38, M.39, M.351, L.457, S.458, L.459, G.460, G.461, L.462 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.37, A:C.38, A:G.461 GOL.5: 12 residues within 4Å: Chain B: K.35, G.36, F.37, C.38, M.39, M.351, L.457, S.458, L.459, G.460, G.461, L.462 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.37, B:C.38, B:G.461 GOL.8: 12 residues within 4Å: Chain C: K.35, G.36, F.37, C.38, M.39, M.351, L.457, S.458, L.459, G.460, G.461, L.462 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.37, C:C.38, C:G.461 GOL.11: 12 residues within 4Å: Chain D: K.35, G.36, F.37, C.38, M.39, M.351, L.457, S.458, L.459, G.460, G.461, L.462 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:F.37, D:C.38, D:G.461

4 x MWY: (3aS,4R,5S,6R,8R,9R,9aR,10R)-6-ethyl-5-hydroxy-4,6,9,10-tetramethyl-1-oxodecahydro-3a,9-propanocyclopenta[8]annulen-8-yl [(5-amino-1H-1,2,4-triazol-3-yl)sulfanyl]acetate(Non-covalent)

MWY.3: 12 residues within 4Å: Chain A: R.85, S.99, L.190, I.281, F.284, A.285, Y.287, E.288, T.289, A.350, L.462 Ligands: HEM.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.281, A:F.284, A:A.285, A:T.289 Hydrogen bonds: A:S.99, A:L.190 Salt bridges: A:E.288 MWY.6: 12 residues within 4Å: Chain B: R.85, S.99, L.190, I.281, F.284, A.285, Y.287, E.288, T.289, A.350, L.462 Ligands: HEM.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.281, B:F.284, B:A.285, B:T.289 Hydrogen bonds: B:S.99, B:L.190 Salt bridges: B:E.288 MWY.9: 12 residues within 4Å: Chain C: R.85, S.99, L.190, I.281, F.284, A.285, Y.287, E.288, T.289, A.350, L.462 Ligands: HEM.7 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.281, C:F.284, C:A.285, C:T.289 Hydrogen bonds: C:S.99, C:L.190 Salt bridges: C:E.288 MWY.12: 12 residues within 4Å: Chain D: R.85, S.99, L.190, I.281, F.284, A.285, Y.287, E.288, T.289, A.350, L.462 Ligands: HEM.10 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.281, D:F.284, D:A.285, D:T.289 Hydrogen bonds: D:S.99, D:L.190 Salt bridges: D:E.288

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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