SMTL ID : 3wb5.1

Crystal Structure of beta secetase in complex with (6S)-2-amino-3,6-dimethyl-6-[(1R,2R)-2-phenylcyclopropyl]-3,4,5,6-tetrahydropyrimidin-4-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

IOD.1: 3 residues within 4Å: Chain A: R.119, E.157, Q.166 Ligand excluded by PLIP IOD.2: 3 residues within 4Å: Chain A: H.68, E.127, S.128 Ligand excluded by PLIP IOD.3: 1 residues within 4Å: Chain A: R.372 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: H.204, Y.207, T.208, G.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.204, A:Y.207 GOL.5: 11 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 Ligands: DMS.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.34, A:G.36, A:Y.37, A:T.255

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 8 residues within 4Å: Chain A: G.34, Q.35, G.36, L.53, G.253, T.255 Ligands: GOL.5, 0B4.7 No protein-ligand interaction detected (PLIP)

1 x 0B4: (6S)-2-amino-3,6-dimethyl-6-[(1R,2R)-2-phenylcyclopropyl]-5,6-dihydropyrimidin-4(3H)-one(Non-covalent)

0B4.7: 11 residues within 4Å: Chain A: L.53, D.55, G.57, S.58, Y.94, F.131, I.141, D.251, G.253, T.254 Ligands: DMS.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.53, A:Y.94, A:Y.94, A:F.131, 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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