SMTL ID : 7kvs.1

Human CYP3A4 bound to an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 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, I.281, F.282, A.285, 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: X74.5 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: 27 residues within 4Å: Chain B: R.85, I.98, S.99, W.106, R.110, I.281, F.282, A.285, 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: X74.9 17 PLIP interactions: 17 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 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.394 Salt bridges: A:H.304, A:K.393

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: K.35, G.36, F.37, C.38, M.39, L.457, S.458, G.460, G.461, L.463 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 GOL.7: 1 residues within 4Å: Chain B: S.119 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.119, B:S.119

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

EDO.4: 5 residues within 4Å: Chain A: Q.58, Q.59, P.60, K.370, G.371 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.58, A:K.370 EDO.6: 3 residues within 4Å: Chain A: R.110, G.418, N.421 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.110, A:G.418, A:N.421

2 x X74: tert-butyl [(2R)-1-(naphthalen-1-yl)-3-{[(2R)-1-oxo-3-phenyl-1-{[3-(pyridin-3-yl)propyl]amino}propan-2-yl]sulfanyl}propan-2-yl]carbamate(Non-covalent)

X74.5: 15 residues within 4Å: Chain A: R.85, R.86, F.88, S.99, L.190, L.191, F.221, I.281, F.284, A.285, T.289, A.350, R.352, E.354 Ligands: HEM.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.88, A:L.190, A:L.190, A:L.191, A:F.221, A:F.221, A:I.281, A:I.281, A:F.284, A:F.284, A:F.284, A:A.285, A:T.289, A:A.350 Hydrogen bonds: A:S.99, A:E.354 X74.9: 15 residues within 4Å: Chain B: R.85, R.86, F.88, S.99, L.190, L.191, F.221, I.281, F.284, A.285, T.289, A.350, R.352, E.354 Ligands: HEM.8 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.88, B:L.190, B:L.190, B:L.191, B:I.281, B:I.281, B:F.284, B:F.284, B:A.285, B:T.289, B:A.350 Hydrogen bonds: B:S.99, B:E.354 pi-Stacking: B:F.221

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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