SMTL ID : 3uqx.1

Crystal structure of BACE1 with its inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x ZPZ: N-[(1R)-1-(4-fluorophenyl)ethyl]-N'-[(2S,3S)-3-hydroxy-4-{4-[(1S)-1-hydroxyethyl]-1H-1,2,3-triazol-1-yl}-1-phenylbutan-2-yl]-5-[methyl(methylsulfonyl)amino]benzene-1,3-dicarboxamide(Non-covalent)

ZPZ.1: 31 residues within 4Å: Chain A: G.51, Q.52, G.53, Y.54, L.70, D.72, G.74, P.110, Y.111, T.112, Q.113, F.148, I.150, W.155, I.158, I.166, Y.238, D.268, S.269, G.270, T.271, T.272, N.273, R.275, R.347, S.365, A.375, E.379 Ligands: URE.9, URE.11, CL.13 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:L.70, A:L.70, A:Y.111, A:Y.111, A:Q.113, A:F.148, A:F.148, A:I.150, A:W.155, A:W.155, A:I.166, A:Y.238, A:A.375 Hydrogen bonds: A:D.72, A:T.112, A:T.112, A:Q.113, A:Q.113, A:G.270, A:G.270, A:G.270, A:T.272, A:N.273, A:S.365 Water bridges: A:P.110, A:Y.111, A:T.272, A:T.272, A:R.275 pi-Stacking: A:Y.111 Halogen bonds: A:E.379

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

SO4.2: 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 SO4.3: 2 residues within 4Å: Chain A: R.101 Ligands: URE.6 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.101 SO4.4: 6 residues within 4Å: Chain A: T.112, R.275, Q.366, S.367, S.368, T.369 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.368, A:S.368, A:T.369 Water bridges: A:R.275 Salt bridges: A:R.275

7 x URE: UREA(Non-functional Binders)

URE.5: 2 residues within 4Å: Chain A: D.102, R.104 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.102, A:R.104 URE.6: 3 residues within 4Å: Chain A: R.101, D.102 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.102, A:D.102 URE.7: 4 residues within 4Å: Chain A: V.107, Y.108, R.168, P.169 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.108, A:Y.108, A:R.168 URE.8: 3 residues within 4Å: Chain A: S.62, P.63, S.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.62, A:S.98 Water bridges: A:S.62 URE.9: 5 residues within 4Å: Chain A: Y.238, K.264, T.369, V.372 Ligands: ZPZ.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.238, A:K.264, A:T.369, A:T.369 URE.10: 2 residues within 4Å: Chain A: F.87, K.147 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.147, A:F.148 URE.11: 2 residues within 4Å: Chain A: S.365 Ligands: ZPZ.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.275, A:R.275, A:R.275

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 3 residues within 4Å: Chain A: S.62, P.63, P.64 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: T.112, T.271, R.275 Ligands: ZPZ.1 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Y.C. et al., Flexibility of the Flap in the Active Site of BACE1 as Revealed by Crystal Structures and MD simulations. to be published

Release Date

2012-11-21

Peptides

Beta-secretase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-secretase 1

Related Entries With Identical Sequence