SMTL ID : 3udh.1

Crystal Structure of BACE with Compound 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x 091: (3S)-spiro[indole-3,3'-pyrrolidin]-2(1H)-one(Non-covalent)

091.1: 11 residues within 4Å: Chain A: L.34, D.36, G.38, Y.75, Q.77, F.112, W.119, I.122, D.232, G.234, T.235 11 PLIP interactions: 11 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:D.232, A:T.235 Water bridges: A:T.76, A:Q.77

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

EDO.2: 7 residues within 4Å: Chain A: T.86, R.100, A.101, N.102, E.138, S.143, Q.147 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.143, A:S.143, A:Q.147 Water bridges: A:N.102, A:K.146 EDO.3: 3 residues within 4Å: Chain A: K.222, E.223, Y.226 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.223, A:E.223 EDO.5: 6 residues within 4Å: Chain A: Y.202, K.228, I.230, R.239, T.333, V.336 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.202, A:K.228, A:R.239, A:T.333 Water bridges: A:T.333, A:G.334 EDO.6: 6 residues within 4Å: Chain A: G.15, Q.16, G.17, I.114, G.234, T.236 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.236, A:T.236 Water bridges: A:G.17 EDO.7: 9 residues within 4Å: Chain A: G.124, L.125, A.126, Y.127, 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.141, A:D.142, A:R.351, A:R.351 Water bridges: A:A.128 EDO.8: 11 residues within 4Å: Chain A: G.45, A.46, A.47, P.48, H.49, L.52, I.106, T.107, E.108, S.109, F.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.46, A:A.47, A:I.106, A:S.109

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 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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