SMTL ID : 6bdi.1

Crystal structure of human CYP3A4 bound to an inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.57 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: DEJ.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:L.353, A:F.415, A:F.415, A:I.423, A:F.427 Hydrogen bonds: A:S.417 Water bridges: A:E.354 Salt bridges: A:R.85, A:R.85, A:R.110, A:R.355, A:R.420 Metal complexes: A:C.422 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: DEJ.4 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:L.353, B:F.415, B:F.415, B:I.423, B:F.427 Hydrogen bonds: B:S.417 Water bridges: B:E.354 Salt bridges: B:R.85, B:R.85, B:R.110, B:R.355, B:R.420 Metal complexes: B:C.422

2 x DEJ: tert-butyl [(2S)-1-(1H-indol-3-yl)-3-{[(2R)-3-oxo-2-[(propan-2-yl)amino]-3-{[(pyridin-3-yl)methyl]amino}propyl]sulfanyl}propan-2-yl]carbamate(Non-covalent)

DEJ.2: 14 residues within 4Å: Chain A: R.85, S.99, R.192, F.193, F.195, I.281, F.284, A.285, T.289, I.349, A.350, R.352, E.354 Ligands: HEM.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:R.192, A:F.195, A:F.284, A:A.285, A:I.349 Hydrogen bonds: A:S.99, A:R.352 Water bridges: A:E.354 DEJ.4: 14 residues within 4Å: Chain B: R.85, S.99, R.192, F.193, F.195, I.281, F.284, A.285, T.289, I.349, A.350, R.352, E.354 Ligands: HEM.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:R.192, B:F.195, B:F.284, B:A.285, B:I.349 Hydrogen bonds: B:S.99, B:R.352 Water bridges: B:E.354

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Samuels, E.R. et al., Interaction of the rationally designed ritonavir-like inhibitors with human cytochrome P450 3A4: Impact of the side group interplay. Mol. Pharm. (2017)

Release Date

2017-12-13

Peptides

Cytochrome P450 3A4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytochrome P450 3A4

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