SMTL ID : 9cox.1

Crystal structure of CYP3A4 bound to an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.72 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: 01.2 19 PLIP interactions: 19 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:I.349, A:A.350, 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: 29 residues within 4Å: Chain B: 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: 01.4 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:I.98, B:F.117, B:I.281, B:F.282, B:A.285, B:V.293, B:I.349, 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

2 x 01: N-[(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]pyridine-3-carboxamide

01.2: 11 residues within 4Å: Chain A: R.85, F.88, M.94, S.99, I.100, I.281, F.284, A.285, T.289, L.462 Ligands: HEM.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.88, A:M.94, A:I.281, A:F.284, A:F.284, A:A.285, A:T.289, A:L.462 Hydrogen bonds: A:S.99 01.4: 11 residues within 4Å: Chain B: R.85, F.88, M.94, S.99, I.100, I.281, F.284, A.285, T.289, L.462 Ligands: HEM.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.88, B:M.94, B:I.281, B:F.284, B:F.284, B:A.285, B:T.289, B:L.462 Hydrogen bonds: B:S.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Samuels, E.R. et al., Evaluation of larger side-group functionalities and the side/end-group interplay in ritonavir-like inhibitors of CYP3A4. Chem.Biol.Drug Des. (2025)

Release Date

2025-01-08

Peptides

Cytochrome P450 3A4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytochrome P450 3A4

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