SMTL ID : 6bdk.1

Crystal structure of human CYP3A4 bound to an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.67 Å

Oligo State

homo-tetramer

Ligands

4 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: DJ1.2 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:I.98, A:F.117, A:F.282, A:A.285, 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 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: DJ1.4 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:I.98, B:F.117, B:F.282, B:A.285, 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 Salt bridges: B:R.85, B:R.85, B:R.110, B:R.355, B:R.420 Metal complexes: B:C.422 HEM.5: 28 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, F.427, A.428, M.432 Ligands: DJ1.6 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:I.98, C:F.117, C:F.282, C:A.285, C:V.293, C:I.349, C:A.350, C:L.353, C:F.415, C:F.415, C:I.423, C:F.427 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: 28 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, F.427, A.428, M.432 Ligands: DJ1.8 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:I.98, D:F.117, D:F.282, D:A.285, D:V.293, D:I.349, D:A.350, D:L.353, D:F.415, D:F.415, D:I.423, D:F.427 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 DJ1: tert-butyl [(2S)-1-{[(2R)-2-(cyclopentylamino)-3-oxo-3-{[(pyridin-3-yl)methyl]amino}propyl]sulfanyl}-3-(1H-indol-3-yl)propan-2-yl]carbamate(Non-covalent)

DJ1.2: 16 residues within 4Å: Chain A: R.85, F.88, S.99, I.100, 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 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.88, A:R.192, A:F.193, A:F.195, A:F.195, A:F.284, A:F.284, A:A.285, A:I.349 Hydrogen bonds: A:S.99, A:S.99, A:A.350 DJ1.4: 16 residues within 4Å: Chain B: R.85, F.88, S.99, I.100, 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 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.88, B:R.192, B:F.193, B:F.195, B:F.195, B:F.284, B:F.284, B:A.285, B:I.349 Hydrogen bonds: B:S.99, B:S.99, B:A.350 DJ1.6: 16 residues within 4Å: Chain C: R.85, F.88, S.99, I.100, R.192, F.193, F.195, I.281, F.284, A.285, T.289, I.349, A.350, R.352, E.354 Ligands: HEM.5 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.88, C:R.192, C:F.193, C:F.195, C:F.195, C:F.284, C:F.284, C:A.285, C:I.349 Hydrogen bonds: C:S.99, C:S.99, C:A.350 DJ1.8: 16 residues within 4Å: Chain D: R.85, F.88, S.99, I.100, R.192, F.193, F.195, I.281, F.284, A.285, T.289, I.349, A.350, R.352, E.354 Ligands: HEM.7 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:F.88, D:R.192, D:F.193, D:F.195, D:F.195, D:F.284, D:F.284, D:A.285, D:I.349 Hydrogen bonds: D:S.99, D:S.99, D:A.350

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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