SMTL ID : 3vv7.1

Crystal Structure of beta secetase in complex with 2-amino-6-((1S,2R)-2-(3'-methoxybiphenyl-3-yl)cyclopropyl)-3-methylpyrimidin-4(3H)-one

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

IOD.1: 3 residues within 4Å: Chain A: T.126, E.127, S.128 Ligand excluded by PLIP IOD.2: 2 residues within 4Å: Chain A: R.372, R.374 Ligand excluded by PLIP IOD.3: 1 residues within 4Å: Chain A: K.130 Ligand excluded by PLIP IOD.4: 3 residues within 4Å: Chain A: Q.78, L.79, S.81 Ligand excluded by PLIP IOD.5: 3 residues within 4Å: Chain A: R.119, E.157, S.162 Ligand excluded by PLIP IOD.6: 1 residues within 4Å: Chain A: K.261 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: R.73, Y.74, Q.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.74, A:Y.74, A:Q.76 GOL.8: 10 residues within 4Å: Chain A: K.32, S.33, G.34, Q.35, G.36, Y.37, V.193, T.255, A.358, E.362 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.32, A:G.34, A:G.36, A:T.255, A:E.362

1 x 0B1: 2-AMINO-6-[(1S,2R)-2-(3'-METHOXYBIPHENYL-3-YL)CYCLOPROPYL]-3-METHYLPYRIMIDIN-4(3H)-ONE(Non-covalent)

0B1.9: 15 residues within 4Å: Chain A: G.34, Q.35, G.36, L.53, V.54, D.55, G.57, S.58, Y.94, F.131, I.141, D.251, S.252, G.253, T.254 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.53, A:D.55, A:Y.94, A:Y.94, A:F.131, A:I.141 Hydrogen bonds: A:G.253 Water bridges: A:T.95 Salt bridges: A:D.55, A:D.251

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yonezawa, S. et al., Conformational restriction approach to beta-secretase (BACE1) inhibitors: effect of a cyclopropane ring to induce an alternative binding mode. J.Med.Chem. (2012)

Release Date

2012-10-24

Peptides

Beta-secretase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-secretase 1

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