SMTL ID : 6bd6.1

Crystal structure of human CYP3A4 bound to an inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 27 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, A.428, M.432 Ligands: 80K.2 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:I.98, A:F.117, A:F.282, A:A.285, A:T.289, A:V.293, A:I.349, A:I.349, A:A.350, A:L.353, A:F.415, A:F.415 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: 27 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, A.428, M.432 Ligands: 80K.4 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:I.98, B:F.117, B:F.282, B:A.285, B:T.289, B:V.293, B:I.349, B:I.349, B:A.350, B:L.353, B:F.415, B:F.415 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.5: 27 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, A.428, M.432 Ligands: 80K.6 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:I.98, C:F.117, C:F.282, C:A.285, C:T.289, C:V.293, C:I.349, C:I.349, C:A.350, C:L.353, C:F.415, C:F.415 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.7: 27 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, A.428, M.432 Ligands: 80K.8 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:I.98, D:F.117, D:F.282, D:A.285, D:T.289, D:V.293, D:I.349, D:I.349, D:A.350, D:L.353, D:F.415, D:F.415 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 80K: tert-butyl (2-{[(2S)-3-oxo-2-(phenylamino)-3-{[(pyridin-3-yl)methyl]amino}propyl]sulfanyl}ethyl)carbamate(Non-covalent)

80K.2: 12 residues within 4Å: Chain A: R.85, F.88, S.99, I.100, F.193, F.221, I.280, I.281, F.284, A.285, T.289 Ligands: HEM.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.193, A:I.281, A:F.284, A:F.284, A:F.284, A:F.284, A:F.284, A:A.285 Hydrogen bonds: A:S.99 pi-Stacking: A:F.221 80K.4: 12 residues within 4Å: Chain B: R.85, F.88, S.99, I.100, F.193, F.221, I.280, I.281, F.284, A.285, T.289 Ligands: HEM.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.193, B:I.281, B:F.284, B:F.284, B:F.284, B:F.284, B:F.284, B:A.285 Hydrogen bonds: B:S.99 pi-Stacking: B:F.221 80K.6: 12 residues within 4Å: Chain C: R.85, F.88, S.99, I.100, F.193, F.221, I.280, I.281, F.284, A.285, T.289 Ligands: HEM.5 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.193, C:I.281, C:F.284, C:F.284, C:F.284, C:F.284, C:F.284, C:A.285 Hydrogen bonds: C:S.99 pi-Stacking: C:F.221 80K.8: 12 residues within 4Å: Chain D: R.85, F.88, S.99, I.100, F.193, F.221, I.280, I.281, F.284, A.285, T.289 Ligands: HEM.7 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.193, D:I.281, D:F.284, D:F.284, D:F.284, D:F.284, D:F.284, D:A.285 Hydrogen bonds: D:S.99 pi-Stacking: D:F.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Samuels, E.R. et al., Inhibition of Human CYP3A4 by Rationally Designed Ritonavir-Like Compounds: Impact and Interplay of the Side Group Functionalities. Mol Pharm. (2018)

Release Date

2017-12-13

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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