SMTL ID : 7kvq.1

Human CYP3A4 bound to an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

2 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, I.281, 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: X7D.7 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:I.98, A:F.117, A:I.281, 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.8: 26 residues within 4Å: Chain B: R.85, I.98, S.99, W.106, R.110, I.281, 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 Ligands: X7D.9 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:I.98, B:I.281, B:F.282, B:A.285, B:V.293, B:I.349, B:A.350, B:F.415, B:I.423, B:F.427, B:A.428 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

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: H.304, E.392, K.393, F.394 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.394 Salt bridges: A:H.304

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: Q.309, Q.312, E.313, R.476 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.313

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: P.21, F.40, E.43, C.44, K.47, Y.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.43, A:Y.48 EDO.5: 8 residues within 4Å: Chain A: Y.132, V.135, L.136, A.158, Y.159, D.162, D.174, N.177 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.132, A:D.174, A:D.174, A:N.177 EDO.6: 9 residues within 4Å: Chain A: K.35, G.36, F.37, C.38, M.39, M.351, S.458, G.460, G.461 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.35, A:F.37, A:C.38, A:M.39, A:G.461

2 x X7D: tert-butyl [(2S)-1-(naphthalen-1-yl)-3-{[(2S)-1-oxo-3-phenyl-1-{[3-(pyridin-3-yl)propyl]amino}propan-2-yl]sulfanyl}propan-2-yl]carbamate(Non-covalent)

X7D.7: 14 residues within 4Å: Chain A: R.85, R.86, F.88, S.99, I.100, L.191, F.221, I.281, F.284, A.285, T.289, A.350, E.354 Ligands: HEM.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:R.86, A:F.88, A:L.191, A:F.221, A:I.281, A:I.281, A:F.284, A:F.284, A:A.285, A:T.289, A:A.350 Hydrogen bonds: A:R.86, A:S.99 pi-Stacking: A:F.221 X7D.9: 15 residues within 4Å: Chain B: R.86, F.88, S.99, I.100, L.190, L.191, F.221, I.281, F.284, A.285, T.289, A.350, R.352, E.354 Ligands: HEM.8 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:R.86, B:L.190, B:L.191, B:L.191, B:F.221, B:I.281, B:F.284, B:F.284, B:F.284, B:A.285, B:T.289, B:A.350 Hydrogen bonds: B:S.99, B:E.354 pi-Cation interactions: B:R.85

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
B

Cytochrome P450 3A4

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