SMTL ID : 5ygx.1

Structure of BACE1 in complex with N-(3-((4R,5R,6S)-2-amino-6-(1,1-difluoroethyl)-5-fluoro-4-methyl-5,6-dihydro-4H-1,3-oxazin-4-yl)-4-fluorophenyl)-5-(fluoromethoxy)pyrazine-2-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

IOD.1: 3 residues within 4Å: Chain A: H.68, E.127, S.128 Ligand excluded by PLIP IOD.2: 3 residues within 4Å: Chain A: H.68, D.129, K.130 Ligand excluded by PLIP

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: R.73, Y.74, Q.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.74, A:Y.74 GOL.4: 7 residues within 4Å: Chain A: G.57, S.58, V.92, Y.94, R.151, Y.221 Ligands: 0B5.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.57, A:R.151, A:Y.221 Water bridges: A:S.59 GOL.5: 5 residues within 4Å: Chain A: S.109, I.110, P.111, P.114, N.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.109, A:S.109, A:I.110 GOL.6: 4 residues within 4Å: Chain A: H.204, Y.207, T.208, G.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.204 Water bridges: A:G.209 GOL.7: 5 residues within 4Å: Chain A: R.77, Q.78, S.80, S.81, Y.83 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.83

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

DMS.8: 4 residues within 4Å: Chain A: R.119, N.121, E.157, Q.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.121, A:S.162 Salt bridges: A:E.157

1 x 0B5: ~{N}-[3-[(4~{R},5~{R},6~{S})-2-azanyl-6-[1,1-bis(fluoranyl)ethyl]-5-fluoranyl-4-methyl-5,6-dihydro-1,3-oxazin-4-yl]-4-fluoranyl-phenyl]-5-(fluoranylmethoxy)pyrazine-2-carboxamide(Non-covalent)

0B5.9: 19 residues within 4Å: Chain A: G.34, Q.35, G.36, Y.37, L.53, D.55, G.57, Y.94, F.131, I.133, I.141, D.251, S.252, G.253, T.254, T.255, R.330, A.358 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.94 Hydrogen bonds: A:G.36, A:D.55, A:G.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakahara, K. et al., Discovery of Potent and Centrally Active 6-Substituted 5-Fluoro-1,3-dihydro-oxazine beta-Secretase (BACE1) Inhibitors via Active Conformation Stabilization. J. Med. Chem. (2018)

Release Date

2018-08-08

Peptides

Beta-secretase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-secretase 1

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