SMTL ID : 4jlt.1

Crystal structure of P450 2B4(H226Y) in complex with paroxetine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

monomer

Ligands

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

HEM.1: 26 residues within 4Å: Chain A: R.79, V.94, I.95, W.102, R.106, I.160, A.279, G.280, T.283, T.284, T.287, Q.338, I.344, V.348, H.350, L.373, P.409, F.410, S.411, R.415, C.417, L.418, G.419, I.422, A.423 Ligands: 8PR.5 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:V.94, A:I.95, A:I.160, A:T.283, A:I.344, A:V.348, A:L.373, A:F.410, A:F.410, A:L.418, A:I.422 Hydrogen bonds: A:I.95, A:S.411, A:S.411 Water bridges: A:V.348 Salt bridges: A:R.79, A:R.79, A:R.106, A:H.350, A:R.415 Metal complexes: A:C.417

3 x CM5: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE(Non-covalent)

CM5.2: 10 residues within 4Å: Chain A: S.157, F.165, K.167, F.169, F.176, L.179, F.183, F.225, F.277 Ligands: PO4.12 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.165, A:F.176, A:L.179, A:F.183, A:F.225, A:F.277, A:F.277 Hydrogen bonds: A:K.167, A:K.167, A:K.232 CM5.3: 5 residues within 4Å: Chain A: E.231, L.250, M.253, E.254, H.266 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.254, A:E.254 Hydrogen bonds: A:E.231, A:H.266 CM5.4: 11 residues within 4Å: Chain A: L.24, L.25, M.27, D.28, R.29, G.31, L.32, F.193, Q.196, V.197, L.200 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.24, A:R.29, A:F.193, A:V.197, A:L.200 Hydrogen bonds: A:L.25

1 x 8PR: Paroxetine(Non-covalent)

8PR.5: 14 residues within 4Å: Chain A: I.82, I.95, F.187, E.199, F.278, A.279, E.282, F.346, G.347, V.348, P.349, F.370, V.458 Ligands: HEM.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.278, A:A.279, A:F.346, A:V.348, A:V.458 Hydrogen bonds: A:E.199, A:E.282

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 2 residues within 4Å: Chain A: R.472, H.473 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.473 Salt bridges: A:R.472 SO4.7: 2 residues within 4Å: Chain A: H.300, R.304 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.300, A:R.304 SO4.8: 2 residues within 4Å: Chain A: R.324, A.325 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.324, A:A.325, A:R.424, A:R.424 Salt bridges: A:R.324 SO4.9: 4 residues within 4Å: Chain A: T.385, P.386, N.387, T.388 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.387, A:N.387, A:T.388

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: D.71, Q.72, A.73, E.74, A.75, K.414 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.73, A:E.74, A:A.75, A:K.414, A:K.414 Water bridges: A:K.354, A:K.354

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.11: 3 residues within 4Å: Chain A: S.194, G.210, T.211 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.194, A:S.194, A:T.211 PO4.12: 5 residues within 4Å: Chain A: F.165, S.229, K.232, H.233 Ligands: CM5.2 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.232 Salt bridges: A:K.232, A:H.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shah, M.B. et al., A Structural Snapshot of CYP2B4 in Complex with Paroxetine Provides Insights into Ligand Binding and Clusters of Conformational States. J.Pharmacol.Exp.Ther. (2013)

Release Date

2013-06-26

Peptides

Cytochrome P450 2B4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytochrome P450 2B4

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