SMTL ID : 4x2l.1

Crystal structure of human BACE-1 bound to Compound 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

monomer

Ligands

1 x 3WP: (4S)-4-(2,4-difluorophenyl)-4-methyl-5,6-dihydro-4H-1,3-thiazin-2-amine(Non-covalent)

3WP.1: 12 residues within 4Å: Chain A: L.46, D.48, G.50, S.51, Y.87, F.124, W.131, I.134, D.244, G.246, T.247 Ligands: DMS.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.46, A:F.124 Hydrogen bonds: A:D.244, A:T.247

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

IOD.2: 4 residues within 4Å: Chain A: H.61, T.119, E.120, S.121 Ligand excluded by PLIP IOD.3: 1 residues within 4Å: Chain A: F.63 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 1 residues within 4Å: Chain A: S.344 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.344 Water bridges: A:R.251, A:S.344 NA.5: 2 residues within 4Å: Chain A: H.197, Y.200 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.197

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 11 residues within 4Å: Chain A: K.25, G.27, Q.28, G.29, Y.30, S.245, T.247, T.248, A.351, E.355 Ligands: DMS.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.27, A:G.29, A:T.247 Water bridges: A:Y.30 GOL.7: 4 residues within 4Å: Chain A: L.165, I.195, R.365, R.367 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.365, A:R.365, A:R.367 GOL.8: 4 residues within 4Å: Chain A: V.83, Y.84, R.144, P.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.84

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

DMS.9: 6 residues within 4Å: Chain A: T.98, R.112, A.113, N.114, E.150, Q.159 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.114 Salt bridges: A:E.150 DMS.10: 8 residues within 4Å: Chain A: G.27, Q.28, G.29, I.126, G.246, T.248 Ligands: 3WP.1, GOL.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Butler, C.R. et al., Discovery of a Series of Efficient, Centrally Efficacious BACE1 Inhibitors through Structure-Based Drug Design. J.Med.Chem. (2015)

Release Date

2015-03-04

Peptides

Beta-secretase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-secretase 1

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