SMTL ID : 3wb4.1

Crystal Structure of beta secetase in complex with 2-amino-3,6-dimethyl-6-(2-phenylethyl)-3,4,5,6-tetrahydropyrimidin-4-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.34, A:G.36 Water bridges: A:T.255 GOL.2: 5 residues within 4Å: Chain A: E.40, T.49, N.51, R.73, N.137 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.40, A:N.51, A:R.73, A:R.73, A:N.137 GOL.3: 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.4: 3 residues within 4Å: Chain A: H.204, Y.207, G.209 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.204

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

IOD.5: 1 residues within 4Å: Chain A: R.119 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: K.98, E.127 Ligand excluded by PLIP

1 x 0B3: (6R)-2-amino-3,6-dimethyl-6-(2-phenylethyl)-5,6-dihydropyrimidin-4(3H)-one(Non-covalent)

0B3.7: 12 residues within 4Å: Chain A: L.53, D.55, G.57, S.58, Y.94, F.131, I.133, W.138, I.141, D.251, G.253, T.254 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.53, A:Y.94, A:Y.94, A:I.133, A:W.138, A:I.141 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 III: Effective investigation of the binding mode by combinational use of X-ray analysis, isothermal titration calorimetry and theoretical calculations. Bioorg.Med.Chem. (2013)

Release Date

2013-10-02

Peptides

Beta-secretase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-secretase 1

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