SMTL ID : 9fdi.1

Gcase in complex with small molecule inhibitor 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

monomer

Ligands

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

NAG-NAG-NAG.1: 5 residues within 4Å: Chain A: I.44, N.58, A.59, T.60, Y.61 No protein-ligand interaction detected (PLIP)

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

NAG.2: 1 residues within 4Å: Chain A: N.98 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.98 NAG.3: 1 residues within 4Å: Chain A: N.309 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-covalent)

K.4: 3 residues within 4Å: Chain A: Y.174, N.185, S.187 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.174, A:N.185, H2O.6, H2O.11 K.5: 5 residues within 4Å: Chain A: G.383, K.385, E.388, S.390, F.436 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.383, A:K.385, A:E.388, A:S.390, H2O.4, H2O.12

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

SO4.6: 6 residues within 4Å: Chain A: Y.50, S.51, R.392, S.395, W.396, D.397 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.51, A:S.395, A:W.396, A:D.397 Water bridges: A:R.392, A:R.392 Salt bridges: A:R.392

2 x 01: 4-(phenylmethyl)piperidine

01.7: 7 residues within 4Å: Chain A: R.78, E.80, R.86, S.91, I.522, P.524, H.529 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:R.78 01.8: 10 residues within 4Å: Chain A: P.68, T.69, F.70, Y.79, E.150, R.209, K.464, F.465, P.467, H.490 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.68, A:F.465, A:F.465 Water bridges: A:E.150 pi-Stacking: A:F.70

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

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