SMTL ID : 7ufe.1

Human CYP3A4 bound to an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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.282, A.285, T.289, V.293, L.344, 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: NXR.4 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:I.98, A:F.282, A:A.285, A:V.293, A:L.344, A:I.349, A:A.350, A:F.415, A:F.415, A:I.423, A:F.427 Hydrogen bonds: A:S.417 Water bridges: A:R.85, 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.5: 25 residues within 4Å: Chain B: R.85, I.98, W.106, R.110, F.282, A.285, T.289, V.293, L.344, 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: NXR.7 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:I.98, B:F.282, B:A.285, B:V.293, B:L.344, B:I.349, B:A.350, B:L.353, B:F.415, B:I.423, B:F.427 Hydrogen bonds: B:S.417 Water bridges: B:R.85, 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

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: T.118, G.120, K.121, E.124 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.120, A:K.121, A:E.124, A:E.124 GOL.3: 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:E.392, A:F.394, A:F.394 GOL.6: 3 residues within 4Å: Chain B: H.304, K.393, F.394 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.304, B:F.394

2 x NXR: N-[(2S)-1-{[(2R)-1-oxo-3-phenyl-1-{[3-(pyridin-3-yl)propyl]amino}propan-2-yl]sulfanyl}-3-phenylpropan-2-yl]pyridine-3-carboxamide(Non-covalent)

NXR.4: 13 residues within 4Å: Chain A: R.85, R.86, F.88, S.99, L.190, L.191, F.193, F.221, I.281, F.284, A.285, T.289 Ligands: HEM.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.190, A:L.191, A:L.191, A:F.193, A:F.221, A:I.281, A:I.281, A:F.284, A:F.284, A:F.284, A:A.285, A:T.289 Hydrogen bonds: A:S.99 NXR.7: 10 residues within 4Å: Chain B: R.85, R.86, F.88, S.99, L.190, I.281, F.284, A.285, T.289 Ligands: HEM.5 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.190, B:I.281, B:F.284, B:F.284, B:F.284, B:A.285, B:T.289 Hydrogen bonds: B:S.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Samuels, E.R. et al., Interaction of CYP3A4 with Rationally Designed Ritonavir Analogues: Impact of Steric Constraints Imposed on the Heme-Ligating Group and the End-Pyridine Attachment. Int J Mol Sci (2022)

Release Date

2022-07-27

Peptides

Cytochrome P450 3A4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cytochrome P450 3A4

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