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

BACE-1 in complex with compound #32

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

monomer

Ligands

1 x QKA: (1R,2R)-2-[(4aR,7aR)-2-amino-6-(pyrimidin-2-yl)-4a,5,6,7-tetrahydropyrrolo[3,4-d][1,3]thiazin-7a(4H)-yl]-N-{[(1R,2R)-2-methylcyclopropyl]methyl}cyclopropane-1-carboxamide(Non-covalent)

QKA.1: 20 residues within 4Å: Chain A: S.59, G.60, Q.61, G.62, L.79, D.81, G.83, S.84, V.118, Y.120, W.125, W.164, I.167, R.177, D.277, S.278, G.279, T.280, T.281 Ligands: SO4.7 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.79, A:V.118, A:Y.120, A:I.167, A:R.177 Hydrogen bonds: A:S.84, A:D.277, A:G.279 Water bridges: A:S.85, A:Y.120

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: F.208, G.322, D.367 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.322, A:D.367 GOL.3: 6 residues within 4Å: Chain A: T.131, R.145, N.147, E.183, S.188, Q.192 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.147, A:E.183, A:Q.192 Water bridges: A:T.131, A:T.131, A:E.183 GOL.4: 3 residues within 4Å: Chain A: R.99, Y.100, Q.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.100, A:Y.100

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

SO4.5: 3 residues within 4Å: Chain A: R.356, V.358, K.370 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.356 Salt bridges: A:R.356, A:K.370 SO4.6: 1 residues within 4Å: Chain A: K.288 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.288 SO4.7: 3 residues within 4Å: Chain A: Y.120, T.121 Ligands: QKA.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.121 Water bridges: A:T.121, A:Q.122, A:R.284, A:R.284, A:R.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Winneroski, L.L. et al., Preparation and biological evaluation of BACE1 inhibitors: Leveraging trans-cyclopropyl moieties as ligand efficient conformational constraints. Bioorg.Med.Chem. (2020)

Release Date

2019-12-11

Peptides

Beta-secretase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Beta-secretase 1

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