SMTL ID : 4dh6.1

Structure of Bace-1 (Beta-Secretase) in Complex with (2R)-N-((2S,3R)-1-(benzo[d][1,3]dioxol-5-yl)-3-hydroxy-4-((S)-6'-neopentyl-3',4'-dihydrospiro[cyclobutane-1,2'-pyrano[2,3-b]pyridine]-4'-ylamino)butan-2-yl)-2-methoxypropanamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

IOD.1: 3 residues within 4Å: Chain A: H.64, E.123, S.124 Ligand excluded by PLIP IOD.2: 1 residues within 4Å: Chain A: K.126 Ligand excluded by PLIP IOD.3: 1 residues within 4Å: Chain A: E.153 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: R.368, R.370 Ligand excluded by PLIP IOD.5: 1 residues within 4Å: Chain A: Y.241 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: Y.87, P.148 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: Y.87, P.89 Ligand excluded by PLIP IOD.8: 4 residues within 4Å: Chain A: I.198, H.200, Y.203, L.207 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 10 residues within 4Å: Chain A: K.28, G.30, Q.31, G.32, Y.33, S.248, T.250, T.251, A.354, E.358 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.30, A:Q.31, A:G.32, A:T.250 GOL.10: 2 residues within 4Å: Chain A: R.69, Y.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.70 Water bridges: A:Y.70

1 x 0KN: (2R)-N-[(2S,3R)-1-(1,3-BENZODIOXOL-5-YL)-4-{[(4'S)-6'-(2,2-DIMETHYLPROPYL)-3',4'-DIHYDROSPIRO[CYCLOBUTANE-1,2'-PYRANO[2,3-B]PYRIDIN]-4'-YL]AMINO}-3-HYDROXYBUTAN-2-YL]-2-METHOXYPROPANAMIDE(Non-covalent)

0KN.11: 21 residues within 4Å: Chain A: L.49, D.51, G.53, S.54, V.88, P.89, Y.90, T.91, F.127, I.129, W.134, I.137, I.145, R.147, Y.217, D.247, G.249, T.250, R.254, T.348, V.351 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.49, A:V.88, A:Y.90, A:Y.90, A:F.127, A:I.137, A:I.145, A:V.351 Hydrogen bonds: A:G.53, A:G.53, A:T.91, A:T.91, A:G.249 pi-Stacking: A:Y.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weiss, M.M. et al., Design and preparation of a potent series of hydroxyethylamine containing beta-secretase inhibitors that demonstrate robust reduction of central beta-amyloid. J.Med.Chem. (2012)

Release Date

2012-04-18

Peptides

Beta-secretase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-secretase 1

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