SMTL ID : 7d36.1

Crystal Structure of BACE1 in complex with N-{3-[(3S)-1-amino-5-fluoro-3-methyl-3,4-dihydro-2,6-naphthyridin-3-yl]-4-fluorophenyl}-5-cyano-3-methylpyridine-2-carboxamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

IOD.1: 3 residues within 4Å: Chain A: T.126, E.127, S.128 Ligand excluded by PLIP IOD.2: 2 residues within 4Å: Chain A: H.68, K.130 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain A: R.372, R.374 Ligand excluded by PLIP IOD.4: 1 residues within 4Å: Chain A: K.261 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: R.19, G.20, F.22, P.170, G.200, G.201, I.202 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.19, A:G.20, A:G.200, A:I.202 Water bridges: A:R.19 GOL.6: 3 residues within 4Å: Chain A: Q.48, T.49, R.73 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.49, A:T.49, A:T.49, A:R.73 Water bridges: A:Y.74 GOL.7: 3 residues within 4Å: Chain A: R.73, Y.74, Q.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.74, A:Y.74 Water bridges: A:H.72

1 x GUC: N-[3-[(3S)-1-azanyl-5-fluoranyl-3-methyl-4H-2,6-naphthyridin-3-yl]-4-fluoranyl-phenyl]-5-cyano-3-methyl-pyridine-2-carboxamide(Non-covalent)

GUC.8: 16 residues within 4Å: Chain A: G.34, Q.35, G.36, L.53, D.55, G.57, S.58, Y.94, F.131, I.141, D.251, S.252, G.253, T.254, T.255, A.358 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.131 Hydrogen bonds: A:D.55, A:G.253 Water bridges: A:Q.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakahara, K. et al., Balancing potency and basicity by incorporating fluoropyridine moieties: Discovery of a 1-amino-3,4-dihydro-2,6-naphthyridine BACE1 inhibitor that affords robust and sustained central A beta reduction. Eur.J.Med.Chem. (2021)

Release Date

2021-07-28

Peptides

Beta-secretase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-secretase 1

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