SMTL ID : 3rvi.1

Structure of Bace-1 (Beta-Secretase) in Complex with 2-((2-Amino-6-o-tolylquinolin-3-yl)methyl)-N-(cyclohexylmethyl)pentanamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

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

IOD.1: 3 residues within 4Å: Chain A: T.122, E.123, S.124 Ligand excluded by PLIP IOD.2: 2 residues within 4Å: Chain A: H.64, K.126 Ligand excluded by PLIP IOD.3: 3 residues within 4Å: Chain A: R.115, E.153, S.158 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: 5 residues within 4Å: Chain A: K.28, Q.31, Y.34, S.132, N.133 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain A: Y.87 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 8 residues within 4Å: Chain A: K.28, S.29, G.30, G.32, Y.33, T.251, A.354, E.358 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.32, A:T.251, A:R.326, A:E.358 GOL.9: 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

1 x RVI: (2R)-2-{[2-amino-6-(2-methylphenyl)quinolin-3-yl]methyl}-N-(cyclohexylmethyl)pentanamide(Non-covalent)

RVI.10: 19 residues within 4Å: Chain A: D.51, G.53, S.54, V.88, Y.90, G.93, K.94, W.95, K.126, F.127, I.137, R.147, Y.217, K.243, I.245, D.247, T.250, T.348, V.351 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.90, A:Y.90, A:Y.90, A:Y.90, A:F.127, A:I.137, A:Y.217, A:I.245, A:V.351 Hydrogen bonds: A:D.51, A:G.53, A:Y.217 pi-Stacking: A:Y.90, A:F.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, Y. et al., From Fragment Screening to In Vivo Efficacy: Optimization of a Series of 2-Aminoquinolines as Potent Inhibitors of Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1). J.Med.Chem. (2011)

Release Date

2011-08-31

Peptides

Beta-secretase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-secretase 1

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