SMTL ID : 4d6z.1

Cytochrome P450 3A4 bound to imidazole and an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

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

HEM.1: 28 residues within 4Å: Chain A: R.85, I.98, S.99, W.106, R.110, F.117, 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, A.428, M.432 Ligands: PK9.2, IMD.3 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:I.98, A:F.117, A:F.282, A:V.293, A:I.349, A:A.350, A:L.353, A:F.415, A:F.415, A:I.423 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

1 x PK9: tert-butyl {6-oxo-6-[(pyridin-3-ylmethyl)amino]hexyl}carbamate(Non-covalent)

PK9.2: 13 residues within 4Å: Chain A: R.85, F.88, S.99, R.192, F.193, F.195, I.281, F.284, T.289, I.349, A.350 Ligands: HEM.1, IMD.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.192, A:F.193, A:F.195, A:F.284 Hydrogen bonds: A:S.99, A:S.99 pi-Stacking: A:F.88

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 4 residues within 4Å: Chain A: A.285, T.289 Ligands: HEM.1, PK9.2 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 12 residues within 4Å: Chain A: K.35, G.36, F.37, C.38, M.39, M.351, L.457, S.458, G.460, G.461, L.462, L.463 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.37, A:C.38, A:M.39, A:G.461 GOL.5: 7 residues within 4Å: Chain A: P.21, S.32, F.40, E.43, C.44, K.47, Y.48 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.32, A:E.43, A:E.43, A:Y.48 Water bridges: A:K.47 GOL.6: 6 residues within 4Å: Chain A: P.21, T.22, L.24, N.29, L.31, S.32 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.29, A:N.29 Water bridges: A:T.22, A:L.31 GOL.7: 6 residues within 4Å: Chain A: F.347, Y.379, R.383, E.392, L.455, L.457 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.383, A:R.383, A:E.392

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaur, P. et al., Structure-Based Inhibitor Design for Evaluation of a Cyp3A4 Pharmacophore Model. J.Med.Chem. (2016)

Release Date

2015-09-23

Peptides

CYTOCHROME P450 3A4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CYTOCHROME P450 3A4

Related Entries With Identical Sequence