SMTL ID : 6dmi.1

A multiconformer ligand model of 5T5 bound to BACE-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

2 x NA: SODIUM ION(Non-functional Binders)

NA.1: 2 residues within 4Å: Chain A: H.186, Y.189 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.186 Water bridges: A:Y.189 NA.3: 2 residues within 4Å: Chain A: V.146, T.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.146

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 5 residues within 4Å: Chain A: R.101, N.103, E.139, S.144, Q.148 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.103, A:S.144 Water bridges: A:N.103 Salt bridges: A:E.139

1 x 5T5: [(1~{R},2~{R})-2-[(4~{S})-2-azanyl-4-[4-[bis(fluoranyl)methoxy]phenyl]-5~{H}-1,3-oxazol-4-yl]cyclopropyl]-(5-chloranylpyridin-3-yl)methanone(Non-covalent)

5T5.4: 15 residues within 4Å: Chain A: G.16, G.18, L.35, D.37, G.39, S.40, V.74, Y.76, I.123, R.133, D.233, S.234, G.235, T.236, T.237 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.35, A:Y.76, A:I.123 Hydrogen bonds: A:D.37, A:G.39, A:T.236 Halogen bonds: A:S.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van Zundert, G.C.P. et al., qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. J. Med. Chem. (2018)

Release Date

2018-12-19

Peptides

Beta-secretase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-secretase 1

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