SMTL ID : 6pz4.2 (1 other biounit)

co-crystal structure of BACE with inhibitor AM-6494

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

IOD.1: 2 residues within 4Å: Chain A: E.123, S.124 Ligand excluded by PLIP IOD.2: 4 residues within 4Å: Chain A: H.64, K.126 Chain B: F.66, N.130 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain B: Y.241 Ligands: IOD.9 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain B: E.123, S.124 Ligand excluded by PLIP IOD.8: 4 residues within 4Å: Chain A: F.66, N.130 Chain B: H.64, K.126 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: Y.241 Ligands: IOD.3 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: R.69, Y.70, Q.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.70, A:Y.70 GOL.5: 6 residues within 4Å: Chain A: G.85, Y.87 Chain B: L.286, C.288, T.333, S.334 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.87, A:Y.87, B:T.333 Water bridges: B:L.286 GOL.10: 3 residues within 4Å: Chain B: R.69, Y.70, Q.72 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.70, B:Y.70 GOL.11: 6 residues within 4Å: Chain A: L.286, C.288, T.333, S.334 Chain B: G.85, Y.87 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.333, A:T.333, B:Y.87, B:Y.87 Water bridges: A:L.286

2 x P6J: N-{3-[(1S,5S,6S)-3-amino-1-(methoxymethyl)-5-methyl-2-thia-4-azabicyclo[4.1.0]hept-3-en-5-yl]-4,5-difluorophenyl}-5-[(prop-2-yn-1-yl)oxy]pyrazine-2-carboxamide(Non-covalent)

P6J.6: 20 residues within 4Å: Chain A: K.28, G.30, Q.31, G.32, Y.33, L.49, D.51, G.53, Y.90, F.127, I.129, I.137, D.247, S.248, G.249, T.250, T.251, R.326, A.354 Chain B: K.126 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.33, A:Y.90, A:Y.90, A:I.137 Hydrogen bonds: A:G.32, A:D.247, A:G.249, A:T.250 Water bridges: A:T.251 Halogen bonds: A:F.127 P6J.12: 20 residues within 4Å: Chain A: K.126 Chain B: K.28, G.30, Q.31, G.32, Y.33, L.49, D.51, G.53, Y.90, F.127, I.129, I.137, D.247, S.248, G.249, T.250, T.251, R.326, A.354 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.33, B:Y.90, B:Y.90, B:I.137 Hydrogen bonds: B:G.32, B:D.247, B:G.249 Water bridges: B:T.250 Halogen bonds: B:F.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pettus, L.H. et al., Discovery of AM-6494: A Potent and Orally Efficacious beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) Inhibitor with in Vivo Selectivity over BACE2. J.Med.Chem. (2020)

Release Date

2019-10-23

Peptides

Beta-secretase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-secretase 1

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