SMTL ID : 9f9z.1

Gcase in complex with small molecule inhibitor 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: I.22, N.36, A.37, T.38, Y.39 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.39

2 x K: POTASSIUM ION(Non-covalent)

K.2: 3 residues within 4Å: Chain A: Y.152, N.163, S.165 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.165, H2O.3 K.3: 6 residues within 4Å: Chain A: G.361, S.362, K.363, E.366, S.368, F.414 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.361, A:K.363, A:E.366, A:S.368, H2O.3

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

SO4.4: 6 residues within 4Å: Chain A: Y.28, S.29, R.370, S.373, W.374, D.375 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.29, A:S.373, A:W.374, A:D.375 Salt bridges: A:R.370

1 x 01: (2~{S})-1-(2,6-dimethylphenoxy)propan-2-amine

01.5: 8 residues within 4Å: Chain A: L.84, L.453, V.454, N.459, D.460, L.461, D.462, A.463 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.461 Hydrogen bonds: A:N.459, A:N.459 Water bridges: A:N.459

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Palmer, N. et al., Fragment-Based Discovery of a Series of Allosteric-Binding Site Modulators of beta-Glucocerebrosidase. J.Med.Chem. (2024)

Release Date

2024-07-03

Peptides

Lysosomal acid glucosylceramidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysosomal acid glucosylceramidase