SMTL ID : 7kvi.1

Human CYP3A4 bound to an inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

2 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, F.427, A.428, M.432 Ligands: X7P.3 20 PLIP interactions: 20 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 Water bridges: 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.4: 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, F.427, A.428, M.432 Ligands: X7P.6 20 PLIP interactions: 20 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 Water bridges: 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

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: K.35, G.36, F.37, C.38, M.39, M.351, S.458, L.459, G.460 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.37, A:M.39, A:G.460 GOL.5: 9 residues within 4Å: Chain B: K.35, G.36, F.37, C.38, M.39, M.351, S.458, L.459, G.460 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.37, B:M.39, B:G.460

2 x X7P: tert-butyl [(2R)-1-{[(2S)-1-oxo-3-phenyl-1-{[3-(pyridin-3-yl)propyl]amino}propan-2-yl]sulfanyl}-3-phenylpropan-2-yl]carbamate(Non-covalent)

X7P.3: 11 residues within 4Å: Chain A: F.88, S.99, I.100, F.221, I.281, F.284, A.285, T.289, A.350, G.461 Ligands: HEM.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.88, A:F.221, A:I.281, A:F.284, A:A.285, A:T.289, A:A.350 Hydrogen bonds: A:S.99 X7P.6: 11 residues within 4Å: Chain B: F.88, S.99, I.100, F.221, I.281, F.284, A.285, T.289, A.350, G.461 Ligands: HEM.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.88, B:F.221, B:I.281, B:F.284, B:A.285, B:T.289, B:A.350 Hydrogen bonds: B:S.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Samuels, E.R. et al., Rational Design of CYP3A4 Inhibitors: A One-Atom Linker Elongation in Ritonavir-Like Compounds Leads to a Marked Improvement in the Binding Strength. Int J Mol Sci (2021)

Release Date

2021-01-20

Peptides

Cytochrome P450 3A4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytochrome P450 3A4

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