SMTL ID : 7d5a.1

Crystal Structure of BACE1 in complex with N-{3-[(9S)-7-amino-2,2-difluoro-9-(prop-1-yn-1-yl)-6-oxa-8-azaspiro[3.5]non-7-en-9-yl]-4-fluorophenyl}-5-cyanopyridine-2-carboxamide

Coordinates

PDB Format

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: 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

1 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

1 x GX6: N-[3-[(9S)-7-azanyl-2,2-bis(fluoranyl)-9-prop-1-ynyl-6-oxa-8-azaspiro[3.5]non-7-en-9-yl]-4-fluoranyl-phenyl]-5-cyano-pyridine-2-carboxamide(Non-covalent)

GX6.4: 19 residues within 4Å: Chain A: G.34, Q.35, G.36, L.53, D.55, G.57, S.58, Y.94, W.99, F.131, I.133, W.138, 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:Y.94 Hydrogen bonds: A:D.55, A:G.253 Water bridges: A:G.34, A:T.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujimoto, K. et al., Structure-Based Approaches to Improving Selectivity through Utilizing Explicit Water Molecules: Discovery of Selective beta-Secretase (BACE1) Inhibitors over BACE2. J.Med.Chem. (2021)

Release Date

2021-03-31

Peptides

Beta-secretase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-secretase 1

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