SMTL ID : 3ohh.1 (2 other biounits)

Crystal structure of beta-site app-cleaving enzyme 1 (bace-wt) complex with bms-681889 aka n~1~-butyl-5-cyano- n~3~-((1s,2r)-1-(3,5-difluorobenzyl)-2-hydroxy-3-((3- methoxybenzyl)amino)propyl)-n~1~-methyl-1h-indole-1,3- dicarboxamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

2 x 3HH: N~1~-butyl-5-cyano-N~3~-{(1S,2R)-1-(3,5-difluorobenzyl)-2-hydroxy-3-[(3-methoxybenzyl)amino]propyl}-N~1~-methyl-1H-indole-1,3-dicarboxamide(Non-covalent)

3HH.1: 27 residues within 4Å: Chain A: S.72, G.73, Q.74, G.75, L.92, D.94, G.96, S.97, V.131, P.132, Y.133, T.134, Q.135, G.136, K.169, F.170, I.172, W.177, I.180, Y.260, D.290, S.291, G.292, T.293, T.294, R.297 Ligands: SO4.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.92, A:Y.133, A:F.170, A:I.172, A:I.180, A:Y.260, A:T.293 Hydrogen bonds: A:D.94, A:T.134, A:D.290, A:G.292, A:T.294, A:T.294, A:R.297 Water bridges: A:S.98, A:T.134, A:Q.135, A:T.293, A:N.295, A:S.390 pi-Stacking: A:Y.133 3HH.5: 27 residues within 4Å: Chain B: S.72, G.73, Q.74, G.75, L.92, D.94, G.96, S.97, V.131, P.132, Y.133, T.134, Q.135, G.136, K.169, F.170, I.172, W.177, I.180, Y.260, D.290, S.291, G.292, T.293, T.294, R.297 Ligands: SO4.6 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:L.92, B:Y.133, B:F.170, B:I.172, B:I.180, B:Y.260, B:T.293 Hydrogen bonds: B:D.94, B:T.134, B:T.134, B:D.290, B:G.292, B:T.294 Water bridges: B:S.98, B:Q.135, B:R.190, B:D.290, B:T.294, B:N.295, B:R.297, B:R.297 pi-Stacking: B:Y.133

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

SO4.2: 4 residues within 4Å: Chain A: Q.135, R.297, S.387 Ligands: 3HH.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.135, A:S.387, A:S.387 Salt bridges: A:R.297 SO4.6: 4 residues within 4Å: Chain B: Q.135, R.297, S.387 Ligands: 3HH.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.135, B:S.387 Water bridges: B:R.297 Salt bridges: B:R.297

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: T.144, R.158, N.160, E.196, S.201 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.160 Water bridges: A:R.123, A:T.144, A:N.160, A:E.196, A:Q.205 GOL.4: 2 residues within 4Å: Chain A: G.335, D.380 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.335 Water bridges: A:G.220, A:W.339, A:D.380 GOL.7: 5 residues within 4Å: Chain B: S.120, T.121, Y.122, R.123, R.158 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.121, B:R.123, B:R.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marcin, L.R. et al., Synthesis and SAR of indole-and 7-azaindole-1,3-dicarboxamide hydroxyethylamine inhibitors of BACE-1. Bioorg.Med.Chem.Lett. (2011)

Release Date

2011-04-06

Peptides

Beta-secretase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-secretase 1

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