SMTL ID : 3tpp.1

Crystal structure of BACE1 complexed with an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x 5HA: N-[(1S,2R)-1-BENZYL-3-(CYCLOPROPYLAMINO)-2-HYDROXYPROPYL]-5-[METHYL(METHYLSULFONYL)AMINO]-N'-[(1R)-1-PHENYLETHYL]ISOPHTHALAMIDE(Non-covalent)

5HA.1: 27 residues within 4Å: Chain A: G.51, Q.52, G.53, L.70, D.72, G.74, S.75, Y.111, T.112, Q.113, F.148, I.150, W.155, I.158, Y.238, I.266, D.268, S.269, G.270, T.271, T.272, N.273, R.275, R.347, S.365, A.375 Ligands: CL.9 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: 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:Y.238, A:I.266, A:A.375 Hydrogen bonds: A:G.74, A:G.74, A:T.112, A:T.112, A:Q.113, A:Q.113, A:G.270, A:G.270, A:T.272, A:N.273, A:N.273, A:S.365 Water bridges: A:T.271, A:T.272, A:T.272, A:R.275

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

CL.2: 2 residues within 4Å: Chain A: P.131, N.132 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: T.416, L.417 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: V.133, T.134 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Ligands: URE.10 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: F.39, G.218, I.219 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: Q.113, G.114, K.147 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: R.101, T.122, R.136 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Ligands: 5HA.1 Ligand excluded by PLIP

11 x URE: UREA(Non-functional Binders)

URE.10: 1 residues within 4Å: Ligands: CL.5 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.282, A:E.282, A:K.286 URE.11: 4 residues within 4Å: Chain A: L.253, K.254, M.255, A.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.253, A:L.253 URE.12: 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 Water bridges: A:R.168 URE.13: 7 residues within 4Å: Chain A: H.85, F.87, S.145, D.146, K.147, F.148, F.149 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.145, A:K.147, A:F.148, A:F.149, A:F.149 Water bridges: A:D.146 URE.14: 6 residues within 4Å: Chain A: T.66, L.67, N.68, H.89, R.90, E.156 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.68, A:H.89, A:E.156, A:E.156 URE.15: 5 residues within 4Å: Chain A: L.124, T.134, V.135, R.136, Q.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.134, A:R.136, A:Q.183 URE.16: 2 residues within 4Å: Chain A: T.66, P.128 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.66 Water bridges: A:T.66, A:T.66, A:H.129 URE.17: 3 residues within 4Å: Chain A: F.39, P.187, G.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.217, A:G.217 URE.18: 6 residues within 4Å: Chain A: I.248, N.249, Q.251, S.287, A.290, A.291 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.248, A:I.248, A:N.249 Water bridges: A:S.287 URE.19: 7 residues within 4Å: Chain A: N.249, A.291, N.318, I.319, F.320, P.321, R.406 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.249, A:A.291, A:R.406 Water bridges: A:V.322 URE.20: 5 residues within 4Å: Chain A: T.332, N.333, D.418, M.419, E.420 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.333, A:T.416, A:D.418, A:M.419, A:E.420, A:E.420, A:E.420 Water bridges: A:D.418

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

SO4.21: 3 residues within 4Å: Chain A: Y.91, Q.93, Q.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.91, A:Q.93, A:Q.95, A:Q.95 SO4.22: 4 residues within 4Å: Chain A: R.275, Q.366, S.367, S.368 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.368, A:T.369, A:T.369 Water bridges: A:R.275 Salt bridges: A:R.275

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 molecular dynamics simulations. Acta Crystallogr.,Sect.D (2012)

Release Date

2011-11-23

Peptides

Beta-secretase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-secretase 1

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