SMTL ID : 5te8.1

Crystal structure of the midazolam-bound human CYP3A4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-trimer

Ligands

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

HEM.1: 24 residues within 4Å: Chain A: R.85, I.98, S.99, W.106, R.110, F.282, A.285, G.286, T.289, A.350, L.353, R.355, P.414, F.415, G.416, S.417, R.420, N.421, C.422, I.423, F.427, A.428, M.432 Ligands: 08J.2 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:I.98, A:F.282, A:F.282, A:A.350, A:L.353, A:F.415, A:F.415, A:I.423, A:F.427, 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.3: 25 residues within 4Å: Chain B: R.85, I.98, S.99, W.106, R.110, F.282, A.285, G.286, T.289, T.290, 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 Ligands: 08J.4 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:I.98, B:F.282, B:F.282, B:A.350, B:L.353, B:F.415, B:F.415, B:I.423, B:F.427, B:A.428 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.5: 26 residues within 4Å: Chain C: R.85, I.98, S.99, W.106, R.110, F.282, A.285, G.286, T.289, V.293, L.344, I.349, A.350, L.353, R.355, P.414, F.415, G.416, R.420, N.421, C.422, I.423, F.427, A.428, M.432 Ligands: 08J.6 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:F.282, C:F.282, C:V.293, C:L.344, C:I.349, C:A.350, C:F.415, C:F.415, C:I.423, C:F.427 Salt bridges: C:R.85, C:R.85, C:R.110, C:R.355, C:R.420 Metal complexes: C:C.422

3 x 08J: 8-chloro-6-(2-fluorophenyl)-1-methyl-4H-imidazo[1,5-a][1,4]benzodiazepine(Non-covalent)

08J.2: 11 residues within 4Å: Chain A: R.85, S.99, L.196, D.197, A.285, T.289, I.349, A.350, G.461, L.462 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.196, A:A.285, A:L.462 08J.4: 10 residues within 4Å: Chain B: R.85, S.99, L.196, D.197, A.285, T.289, I.349, A.350, L.462 Ligands: HEM.3 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.196, B:A.285, B:A.350, B:L.462 Hydrogen bonds: B:S.99 08J.6: 10 residues within 4Å: Chain C: R.85, S.99, L.196, D.197, A.285, T.289, I.349, G.461, L.462 Ligands: HEM.5 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.196, C:L.196, C:A.285, C:I.349, C:L.462

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sevrioukova, I.F. et al., Structural basis for regiospecific midazolam oxidation by human cytochrome P450 3A4. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2016-12-07

Peptides

Cytochrome P450 3A4: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Cytochrome P450 3A4

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