SMTL ID : 3udy.1

Crystal Structure of BACE with Compound 11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x 09G: 3-bromo-4-cyanobenzyl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate(Non-covalent)

09G.1: 15 residues within 4Å: Chain A: L.34, D.36, G.38, P.74, Y.75, Q.77, F.112, W.119, I.122, I.130, R.132, Y.202, D.232, G.234, T.235 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.34, A:Y.75, A:F.112, A:F.112, A:W.119, A:I.122 Hydrogen bonds: A:Q.77, A:R.132, A:D.232 pi-Stacking: A:Y.75

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: T.86, R.100, N.102, E.138, S.143, Q.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.138, A:Q.147 EDO.3: 4 residues within 4Å: Chain A: K.222, E.223, Y.226, Y.388 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.223 EDO.6: 8 residues within 4Å: Chain A: G.124, L.125, A.126, P.139, F.140, F.141, D.142, R.351 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.124, A:F.140, A:F.141, A:R.351, A:R.351 Water bridges: A:A.128 EDO.7: 4 residues within 4Å: Chain A: Y.72, K.79, W.80, E.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.79, A:W.80

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 10 residues within 4Å: Chain A: G.15, Q.16, G.17, Y.18, I.114, S.233, G.234, T.235, T.236, A.339 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.15, A:G.17, A:T.236 Water bridges: A:Q.16

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 2 residues within 4Å: Chain A: H.400, H.402 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.400, A:H.402

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Efremov, I.V. et al., Discovery and optimization of a novel spiropyrrolidine inhibitor of {beta}-secretase (BACE1) through fragment-based drug design. J.Med.Chem. (2012)

Release Date

2012-04-18

Peptides

Beta-secretase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-secretase 1

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