SMTL ID : 8dyc.1

Human CYP3A4 bound to a substrate

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: 26 residues within 4Å: Chain A: R.85, I.98, S.99, W.106, R.110, 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: GOL.3 17 PLIP interactions: 16 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:I.98, A:A.285, A:V.293, 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, H2O.1 HEM.4: 26 residues within 4Å: Chain B: R.85, I.98, S.99, W.106, R.110, 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: GOL.6 17 PLIP interactions: 16 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:I.98, B:A.285, B:V.293, 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, H2O.1

2 x UC7: 2-butyl-6-(butylamino)-1H-benzo[de]isoquinoline-1,3(2H)-dione(Non-covalent)

UC7.2: 15 residues within 4Å: Chain A: F.37, D.56, R.86, P.87, F.88, F.195, F.200, I.203, T.204, P.207, I.210, A.350, M.351, R.352, E.354 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.37, A:F.37, A:F.88, A:I.203, A:P.207, A:I.210, A:R.352 Hydrogen bonds: A:T.204, A:R.352 pi-Stacking: A:F.195, A:F.195 pi-Cation interactions: A:R.86, A:R.86 UC7.5: 15 residues within 4Å: Chain B: F.37, D.56, R.86, P.87, F.88, F.195, F.200, I.203, T.204, P.207, I.210, A.350, M.351, R.352, E.354 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.37, B:F.37, B:F.88, B:I.203, B:P.207, B:I.210, B:R.352 Hydrogen bonds: B:T.204, B:R.352 pi-Stacking: B:F.195, B:F.195 pi-Cation interactions: B:R.86, B:R.86

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: S.99, R.192, I.281, F.284, A.285 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.99, A:R.192, A:R.192 GOL.6: 6 residues within 4Å: Chain B: S.99, R.192, I.281, F.284, A.285 Ligands: HEM.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.99, B:R.192, B:R.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sevrioukova, I.F., Crystal Structure of CYP3A4 Complexed with Fluorol Identifies the Substrate Access Channel as a High-Affinity Ligand Binding Site. Int J Mol Sci (2022)

Release Date

2022-10-26

Peptides

Cytochrome P450 3A4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytochrome P450 3A4

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