SMTL ID : 6c2i.1

Structure of Bace-1 (Beta-Secretase) in complex with : N-(3-((1R,5S,6R)-3-amino-5-methyl-2-oxa-4-azabicyclo[4.1.0]hept-3-en-5-yl)-4-fluorophenyl)-5-methoxypyrazine-2-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

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

IOD.1: 6 residues within 4Å: Chain A: H.64, I.121, T.122, E.123, S.124, F.128 Ligand excluded by PLIP IOD.2: 4 residues within 4Å: Chain A: H.64, F.66, D.125, K.126 Ligand excluded by PLIP IOD.3: 3 residues within 4Å: Chain A: Y.241, K.257, K.258 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: R.69, Y.70, Q.72 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.70 Water bridges: A:H.68, A:Y.70 GOL.5: 3 residues within 4Å: Chain A: G.85, V.86, Y.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.87

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

SO4.6: 4 residues within 4Å: Chain A: L.168, D.365, R.368, R.370 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.370, A:R.370 Salt bridges: A:R.368, A:R.370

1 x EJ7: N-{3-[(1R,5S,6R)-3-amino-5-methyl-2-oxa-4-azabicyclo[4.1.0]hept-3-en-5-yl]-4-fluorophenyl}-5-methoxypyrazine-2-carboxamide(Non-covalent)

EJ7.7: 21 residues within 4Å: Chain A: G.30, Q.31, G.32, Y.33, L.49, D.51, G.53, S.54, Y.90, F.127, I.129, W.134, I.137, D.247, S.248, G.249, T.250, T.251, R.326, A.354, E.358 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.90, A:Y.90, A:F.127, A:I.137 Hydrogen bonds: A:D.51, A:G.249, A:T.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Low, J.D. et al., Diastereoselective synthesis of fused cyclopropyl-3-amino-2,4-oxazine beta-amyloid cleaving enzyme (BACE) inhibitors and their biological evaluation. Bioorg. Med. Chem. Lett. (2018)

Release Date

2018-02-21

Peptides

Beta-secretase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-secretase 1

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