SMTL ID : 3msj.2 (2 other biounits)

Structure of bace (beta secretase) in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x EV3: 3-(2-amino-5-chloro-1H-benzimidazol-1-yl)propan-1-ol(Non-covalent)

EV3.1: 12 residues within 4Å: Chain A: D.51, G.53, S.54, V.88, Y.90, Q.92, W.95, I.245, D.247, G.249, T.250 Ligands: GOL.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.53, A:D.247, A:T.250 Salt bridges: A:D.51, A:D.247 pi-Stacking: A:Y.90

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: S.17, F.18, V.19, E.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.17, A:E.20, A:E.20, A:E.20 GOL.3: 6 residues within 4Å: Chain A: S.105, I.106, P.107, N.111, V.112, T.113 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.106, A:I.106, A:N.111, A:N.111, A:V.112 GOL.4: 5 residues within 4Å: Chain A: E.20, V.22, D.23, N.24, H.108 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.20 Water bridges: A:H.108, A:H.108, A:H.108 GOL.5: 11 residues within 4Å: Chain A: K.28, S.29, G.30, Q.31, G.32, Y.33, V.189, T.251, R.326, A.354, E.358 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.30, A:Q.31, A:G.32, A:G.32, A:E.358 Water bridges: A:G.249 GOL.6: 9 residues within 4Å: Chain A: T.38, V.39, G.40, S.41, P.43, L.103, V.104, S.105, T.113 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.38, A:V.39, A:S.105, A:S.105, A:T.113, A:T.113 Water bridges: A:S.41 GOL.7: 6 residues within 4Å: Chain A: Y.87, K.94, W.95, E.96, E.123, S.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.123 Water bridges: A:E.123 GOL.8: 7 residues within 4Å: Chain A: V.223, R.224, V.225, D.231, K.233, M.234, Y.239 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.225, A:V.225, A:K.233, A:M.234 GOL.9: 6 residues within 4Å: Chain A: L.49, D.51, Q.92, F.127, G.249 Ligands: EV3.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.92, A:F.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Madden, J. et al., Fragment-based discovery and optimization of BACE1 inhibitors. Bioorg.Med.Chem.Lett. (2010)

Release Date

2010-07-14

Peptides

BETA-SECRETASE 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

BETA-SECRETASE 1

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