SMTL ID : 6ung.2 (1 other biounit)

Human CYP3A4 bound to an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 29 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, L.344, 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: QEP.2 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:I.98, A:F.117, A:F.282, A:A.285, A:V.293, A:L.344, A:I.349, A:A.350, A:L.353, A:F.415, A:F.415, 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.3: 29 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, L.344, 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: QEP.4 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:I.98, B:F.117, B:F.282, B:A.285, B:V.293, B:L.344, B:I.349, B:A.350, B:L.353, B:F.415, B:F.415, 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.5: 29 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, L.344, 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: QEP.6 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:I.98, C:F.117, C:F.282, C:A.285, C:V.293, C:L.344, C:I.349, C:A.350, C:L.353, C:F.415, C:F.415, 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.7: 29 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, L.344, 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: QEP.8 21 PLIP interactions: 21 interactions with chain D, Hydrophobic interactions: D:I.98, D:F.117, D:F.282, D:A.285, D:V.293, D:L.344, D:I.349, D:A.350, D:L.353, D:F.415, D:F.415, 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 QEP: tert-butyl [(2S)-1-(naphthalen-1-yl)-3-{[(2R)-3-oxo-2-(phenylamino)-3-{[(pyridin-3-yl)methyl]amino}propyl]sulfanyl}propan-2-yl]carbamate(Non-covalent)

QEP.2: 13 residues within 4Å: Chain A: R.85, F.88, S.99, F.193, F.221, I.280, I.281, F.284, A.285, E.288, T.289, L.462 Ligands: HEM.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.280, A:I.281, A:F.284, A:F.284, A:F.284, A:A.285, A:E.288, A:T.289, A:L.462 Hydrogen bonds: A:S.99, A:F.193 pi-Stacking: A:F.221, A:F.284 QEP.4: 13 residues within 4Å: Chain B: R.85, F.88, S.99, F.193, F.221, I.280, I.281, F.284, A.285, E.288, T.289, L.462 Ligands: HEM.3 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.280, B:I.281, B:F.284, B:F.284, B:F.284, B:A.285, B:E.288, B:T.289, B:L.462 Hydrogen bonds: B:S.99, B:F.193 pi-Stacking: B:F.221, B:F.284 QEP.6: 13 residues within 4Å: Chain C: R.85, F.88, S.99, F.193, F.221, I.280, I.281, F.284, A.285, E.288, T.289, L.462 Ligands: HEM.5 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:I.280, C:I.281, C:F.284, C:F.284, C:F.284, C:A.285, C:E.288, C:T.289, C:L.462 Hydrogen bonds: C:S.99, C:F.193, C:F.193 pi-Stacking: C:F.221, C:F.284 QEP.8: 13 residues within 4Å: Chain D: R.85, F.88, S.99, F.193, F.221, I.280, I.281, F.284, A.285, E.288, T.289, L.462 Ligands: HEM.7 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:I.280, D:I.281, D:F.284, D:F.284, D:F.284, D:A.285, D:E.288, D:T.289, D:L.462 Hydrogen bonds: D:S.99, D:F.193, D:F.193 pi-Stacking: D:F.221, D:F.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Samuels, E.R. et al., An increase in side-group hydrophobicity largely improves the potency of ritonavir-like inhibitors of CYP3A4. Bioorg.Med.Chem. (2020)

Release Date

2020-02-05

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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