SMTL ID : 3vv6.1

Crystal Structure of beta secetase in complex with 2-amino-3-methyl-6-((1S, 2R)-2-phenylcyclopropyl)pyrimidin-4(3H)-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

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

IOD.1: 2 residues within 4Å: Chain A: 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: 1 residues within 4Å: Chain A: K.261 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: R.119, E.157 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: R.73, Y.74, Q.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.74, A:Y.74 GOL.7: 12 residues within 4Å: Chain A: K.32, S.33, G.34, Q.35, G.36, Y.37, V.193, S.252, T.254, T.255, A.358, E.362 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.32, A:G.34, A:G.36, A:T.255 Water bridges: A:T.255, A:T.255, A:E.362 GOL.8: 4 residues within 4Å: Chain A: H.204, Y.207, T.208, G.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.204, A:G.209, A:G.209 GOL.9: 5 residues within 4Å: Chain A: G.34, T.255, N.256, R.330, K.344 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.256, A:N.256, A:R.330 Water bridges: A:G.34, A:T.255, A:T.255

1 x B00: 2-amino-3-methyl-6-[(1S,2R)-2-phenylcyclopropyl]pyrimidin-4(3H)-one(Non-covalent)

B00.10: 8 residues within 4Å: Chain A: D.55, G.57, Y.94, F.131, I.141, D.251, G.253, T.254 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: 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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