SMTL ID : 9fay.1

Gcase in complex with small molecule inhibitor 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

2 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.44, N.58, A.59, T.60, Y.61 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.61 NAG-NAG.2: 2 residues within 4Å: Chain A: Q.182, N.309 No protein-ligand interaction detected (PLIP)

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

NAG.3: 1 residues within 4Å: Chain A: N.98 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.98

2 x K: POTASSIUM ION(Non-covalent)

K.4: 3 residues within 4Å: Chain A: Y.174, N.185, S.187 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:Y.174, A:N.185, H2O.11, H2O.15, H2O.18 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.8, H2O.13

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 5 residues within 4Å: Chain A: T.82, S.84, G.85, R.86, E.89 No protein-ligand interaction detected (PLIP) PEG.9: 10 residues within 4Å: Chain A: P.68, T.69, F.70, S.77, Y.79, K.464, F.465, P.467, H.490, L.532 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.77, A:R.209

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 6 residues within 4Å: Chain A: T.102, G.103, L.104, Q.479, V.507, P.508 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.104, A:P.508 EDO.8: 7 residues within 4Å: Chain A: L.204, V.211, S.212, L.213, K.263, L.264, Q.265 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.211, A:Q.265, A:Q.265 Water bridges: A:L.213

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

SO4.10: 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:W.396, A:D.397, A:D.397 Water bridges: A:R.392, A:R.392 Salt bridges: A:R.392

1 x 01: ~{N}-[(2~{S})-2-azanyl-2-phenyl-ethyl]-3,5-bis(fluoranyl)-~{N}-methyl-benzenesulfonamide

01.11: 11 residues within 4Å: Chain A: H.404, I.407, T.408, L.411, Y.412, N.481, D.482, L.483, D.484, A.485, R.502 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.407, A:D.484 Hydrogen bonds: A:N.481, A:L.483, A:A.485 Water bridges: A:N.481, A:N.481 Halogen bonds: A:H.404

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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