SMTL ID : 3ufl.1

Discovery of Pyrrolidine-based b-Secretase Inhibitors: Lead Advancement through Conformational Design for Maintenance of Ligand Binding Efficiency

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x 508: (1R,4'S)-3,4-dihydro-2H-spiro[naphthalene-1,3'-pyrrolidin]-4'-yl[(2S,4R)-2,4-diphenylpiperidin-1-yl]methanone(Non-covalent)

508.1: 21 residues within 4Å: Chain A: L.34, D.36, G.38, S.39, V.73, P.74, Y.75, Q.77, G.78, K.79, W.80, D.110, K.111, F.112, I.122, I.130, R.132, D.232, G.234, T.235 Ligands: GOL.7 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.34, A:Y.75, A:Y.75, A:Y.75, A:Y.75, A:F.112, A:F.112, A:F.112, A:I.122 Hydrogen bonds: A:D.232

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

SO4.2: 5 residues within 4Å: Chain A: R.239, Q.330, S.331, S.332, T.333 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.76, A:S.332, A:T.333 Salt bridges: A:R.239 SO4.3: 7 residues within 4Å: Chain A: T.86, R.100, A.101, N.102, E.138, S.143, Q.147 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.138, A:S.143, A:Q.147 Water bridges: A:N.102 SO4.4: 2 residues within 4Å: Chain A: R.209, D.216 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.209, A:D.216, A:D.216 Salt bridges: A:R.209 SO4.5: 3 residues within 4Å: Chain A: Y.55, Q.57, Q.59 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.55, A:Q.57, A:Q.59, A:Q.59 Water bridges: A:R.58

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: Y.72, P.74, R.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.72, A:R.132 Water bridges: A:Y.72 GOL.7: 8 residues within 4Å: Chain A: G.15, Q.16, G.17, L.34, I.114, G.234, T.236 Ligands: 508.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.16, A:G.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stachel, S.J. et al., Discovery of pyrrolidine-based beta-secretase inhibitors: Lead advancement through conformational design for maintenance of ligand binding efficiency. Bioorg.Med.Chem.Lett. (2012)

Release Date

2012-01-18

Peptides

Beta-secretase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-secretase 1

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