SMTL ID : 4xxs.1

Crystal structure of BACE1 with a pyrazole-substituted tetrahydropyran thioamidine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

1 x SI5: (4aR,6R,8aS)-8a-(2,4-difluorophenyl)-6-(1-methyl-1H-pyrazol-4-yl)-4,4a,5,6,8,8a-hexahydropyrano[3,4-d][1,3]thiazin-2-amine(Non-covalent)

SI5.1: 17 residues within 4Å: Chain A: D.48, G.50, S.51, V.85, Y.87, Q.89, F.124, I.126, W.131, I.134, I.142, R.144, Y.214, D.244, G.246, T.247 Ligands: DMS.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.87, A:F.124, A:I.134 Hydrogen bonds: A:S.51, A:D.244, A:T.247

2 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 4 residues within 4Å: Chain A: H.61, T.119, E.120, S.121 Ligand excluded by PLIP IOD.3: 1 residues within 4Å: Chain A: K.123 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 12 residues within 4Å: Chain A: K.25, S.26, G.27, Q.28, G.29, Y.30, V.186, T.248, R.323, A.351, E.355 Ligands: DMS.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.25, A:G.27, A:G.29, A:T.248, A:R.323 Water bridges: A:S.26, A:E.355 GOL.8: 9 residues within 4Å: Chain A: T.35, V.36, G.37, S.38, P.40, L.100, V.101, S.102, T.110 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.35, A:L.100, A:S.102, A:S.102

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 2 residues within 4Å: Chain A: K.234, E.235 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:E.235 pi-Cation interactions: A:Y.238 DMS.6: 9 residues within 4Å: Chain A: G.27, Q.28, G.29, L.46, I.126, G.246, T.248 Ligands: SI5.1, GOL.4 No protein-ligand interaction detected (PLIP) DMS.7: 5 residues within 4Å: Chain A: T.98, R.112, N.114, E.150, S.155 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.159 Salt bridges: A:E.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brodney, M.A. et al., Utilizing Structures of CYP2D6 and BACE1 Complexes To Reduce Risk of Drug-Drug Interactions with a Novel Series of Centrally Efficacious BACE1 Inhibitors. J.Med.Chem. (2015)

Release Date

2015-04-01

Peptides

Beta-secretase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-secretase 1

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