SMTL ID : 7d2v.1

Crystal Structure of BACE1 in complex with N-{3-[(5R)-3-amino-2,5-dimethyl-1,1-dioxo-5,6-dihydro-2H-1lambda6,2,4-thiadiazin-5-yl]-4-fluorophenyl}-5-fluoropyridine-2-carboxamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

3 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: R.372, R.374 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain A: H.68, K.130 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 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 GOL.5: 8 residues within 4Å: Chain A: M.311, T.315, N.316, T.399, L.400, D.401, M.402, E.403 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.316, A:D.401, A:M.402 Water bridges: A:N.316, A:D.401, A:E.403, A:E.403

1 x 66F: N-{3-[(5R)-3-amino-2,5-dimethyl-1,1-dioxido-5,6-dihydro-2H-1,2,4-thiadiazin-5-yl]-4-fluorophenyl}-5-fluoropyridine-2-carboxamide(Non-covalent)

66F.6: 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 Hydrogen bonds: A:G.253, A:T.254 Salt bridges: A:D.55, A:D.251

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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