SMTL ID : 3tbg.2 (3 other biounits)

Human cytochrome P450 2D6 with two thioridazines bound in active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

2 x RTZ: 10-{2-[(2R)-1-methylpiperidin-2-yl]ethyl}-2-(methylsulfanyl)-10H-phenothiazine(Non-covalent)

RTZ.1: 15 residues within 4Å: Chain A: L.88, F.90, F.98, L.99, A.187, G.190, L.191, E.194, Q.222, F.225, A.278, D.279, S.282 Ligands: RTZ.2, GOL.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.88, A:F.98, A:F.98, A:L.191, A:L.191, A:E.194, A:A.278 Water bridges: A:L.99 Salt bridges: A:D.279 RTZ.2: 11 residues within 4Å: Chain A: L.51, T.54, V.56, E.194, E.200, L.350, G.351, T.353, I.374, F.461 Ligands: RTZ.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.54, A:V.56, A:L.350, A:L.350, A:T.353, A:F.461 Salt bridges: A:E.200 pi-Stacking: A:F.461

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: C.169, H.236, R.247, D.248, E.251 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.236, A:D.248, A:E.251

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: V.82, T.85, L.88, L.99, E.194, R.199, L.219, Q.222 Ligands: RTZ.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.194, A:R.199, A:R.199, A:Q.222 Water bridges: A:E.194

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.5: 26 residues within 4Å: Chain A: R.79, V.97, F.98, W.106, R.110, L.280, A.283, G.284, T.287, T.288, T.291, Q.342, I.347, V.352, H.354, L.377, P.413, F.414, S.415, R.419, C.421, L.422, G.423, L.426, A.427, E.430 19 PLIP interactions: 18 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.98, A:F.98, A:I.347, A:V.352, A:L.377, A:F.414, A:L.422, A:L.426, A:A.427 Hydrogen bonds: A:F.98, A:S.415, A:S.415 Salt bridges: A:R.79, A:R.79, A:R.110, A:H.354, A:R.419 Metal complexes: A:C.421, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, A. et al., Contributions of Ionic Interactions and Protein Dynamics to Cytochrome P450 2D6 (CYP2D6) Substrate and Inhibitor Binding. J.Biol.Chem. (2015)

Release Date

2012-08-08

Peptides

Cytochrome P450 2D6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Cytochrome P450 2D6

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