SMTL ID : 5ygy.1

Crystal Structure of BACE1 in complex with (S)-N-(3-(2-amino-6-(fluoromethyl)-4 -methyl-4H-1,3-oxazin-4-yl)-4-fluorophenyl)-5-cyanopicolinamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

IOD.1: 4 residues within 4Å: Chain A: H.68, T.126, E.127, S.128 Ligand excluded by PLIP IOD.2: 3 residues within 4Å: Chain A: R.19, R.372, R.374 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain A: H.68, K.130 Ligand excluded by PLIP IOD.4: 3 residues within 4Å: Chain A: R.119, E.157, Q.166 Ligand excluded by PLIP IOD.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: R.73, Y.74, Q.76 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.74, A:Y.74 GOL.7: 5 residues within 4Å: Chain A: P.67, H.68, L.71, Y.74 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.68 GOL.8: 5 residues within 4Å: Chain A: S.33, G.34, T.255, R.330, P.331 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.33, A:G.34, A:R.330, A:R.330

1 x 0B6: ~{N}-[3-[(4~{S})-2-azanyl-6-(fluoranylmethyl)-4-methyl-1,3-oxazin-4-yl]-4-fluoranyl-phenyl]-5-cyano-pyridine-2-carboxamide(Non-covalent)

0B6.9: 18 residues within 4Å: Chain A: G.34, Q.35, G.36, Y.37, L.53, D.55, G.57, S.58, Y.94, F.131, I.133, I.141, D.251, S.252, G.253, T.254, T.255, A.358 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.131 Hydrogen bonds: A:G.57, A:D.251, A:G.253 Water bridges: A:G.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fuchino, K. et al., Rational Design of Novel 1,3-Oxazine Based beta-Secretase (BACE1) Inhibitors: Incorporation of a Double Bond To Reduce P-gp Efflux Leading to Robust A beta Reduction in the Brain. J. Med. Chem. (2018)

Release Date

2018-05-23

Peptides

Beta-secretase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-secretase 1

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