SMTL ID : 9cov.1

Crystal structure of CYP3A4 bound to an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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 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:I.349, A:A.350, 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: 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 20 PLIP interactions: 20 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: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-(1H-indol-3-yl)-3-{[(2R)-1-oxo-3-phenyl-1-{[3-(pyridin-3-yl)propyl]amino}propan-2-yl]sulfanyl}propan-2-yl]pyridine-3-carboxamide

01.2: 10 residues within 4Å: Chain A: F.88, S.99, I.100, I.281, F.284, A.285, T.289, A.350, R.352 Ligands: HEM.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.100, A:I.281, A:I.281, A:F.284, A:F.284, A:A.285, A:T.289, A:A.350 Hydrogen bonds: A:S.99 pi-Cation interactions: A:R.85 01.4: 10 residues within 4Å: Chain B: F.88, S.99, I.100, I.281, F.284, A.285, T.289, A.350, R.352 Ligands: HEM.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.100, 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 pi-Cation interactions: B:R.85

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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