SMTL ID : 4fgx.1 (1 other biounit)

Crystal structure of bace1 with novel inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

1 x 2OP- VAL- GNC- PSA- LEU- ALA- ZAE: Inhibitor (2R,5S,8S,12S,13S,16S,19S,22S)-16-(3-amino-3-oxopropyl)-2,13-dibenzyl-12,22-dihydroxy-8-isobutyl-19-isopropyl-3,5,17-trimethyl-4,7,10,15,18,21-hexaoxo-3,6,9,14,17,20-hexaazatricosan-1-oic acid(Non-covalent)

2OP-VAL-GNC-PSA-LEU-ALA-ZAE.1: 25 residues within 4Å: Chain A: G.51, Q.52, G.53, L.70, D.72, G.74, V.109, P.110, Y.111, T.112, F.148, I.150, W.155, I.158, I.166, R.168, Y.238, K.264, D.268, G.270, T.271, T.272, R.275, T.369 Ligands: URE.5 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:L.70, A:V.109, A:Y.111, A:Y.111, A:T.112, A:F.148, A:I.150, A:W.155, A:I.158, A:I.166, A:T.271 Hydrogen bonds: A:D.72, A:G.74, A:P.110, A:T.112, A:T.112, A:Y.238, A:G.270, A:G.270, A:T.272, A:T.272, A:T.272, A:T.272 Water bridges: A:T.112, A:Q.113, A:N.273, A:R.275 Salt bridges: A:K.264 pi-Stacking: A:Y.111

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 1 residues within 4Å: Chain A: R.101 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.101, A:R.136 Salt bridges: A:R.101 SO4.3: 3 residues within 4Å: Chain A: S.62, P.63, S.98 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.98, A:S.98 SO4.4: 3 residues within 4Å: Chain A: Y.91, Q.93, Q.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.93, A:Q.95, A:Q.95

1 x URE: UREA(Non-functional Binders)

URE.5: 5 residues within 4Å: Chain A: G.51, T.272, R.347, K.361 Ligands: 2OP-VAL-GNC-PSA-LEU-ALA-ZAE.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.347

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

PEG.6: 3 residues within 4Å: Chain A: E.330, R.389, R.391 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.330, A:R.389, A:R.389, A:R.391 Water bridges: A:R.391, A:R.391

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y. et al., Cyanobacterial Peptides as a Prototype for the Design of Potent beta-Secretase Inhibitors and the Development of Selective Chemical Probes for Other Aspartic Proteases. J.Med.Chem. (2012)

Release Date

2013-01-16

Peptides

Beta-secretase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-secretase 1

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