SMTL ID : 9faz.1

Gcase in complex with small molecule inhibitor 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 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: R.250, 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 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.97, A:N.98, A:N.98

2 x K: POTASSIUM ION(Non-covalent)

K.4: 3 residues within 4Å: Chain A: Y.174, N.185, S.187 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:N.185, H2O.4, H2O.8, H2O.9 K.5: 6 residues within 4Å: Chain A: G.383, S.384, K.385, E.388, S.390, F.436 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.383, A:K.385, A:S.390, H2O.4, H2O.11

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

EDO.6: 4 residues within 4Å: Chain A: A.134, L.135, S.136, P.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.134 EDO.8: 7 residues within 4Å: Chain A: L.204, A.207, Q.208, R.209, P.210, V.211 Ligands: DMS.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.207, A:V.211 EDO.9: 1 residues within 4Å: Chain A: G.49 No protein-ligand interaction detected (PLIP) EDO.10: 5 residues within 4Å: Chain A: D.397, M.400, Q.401, H.404, R.502 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.397, A:H.404 Water bridges: A:R.502 EDO.12: 3 residues within 4Å: Chain A: S.84, G.85, R.86 No protein-ligand interaction detected (PLIP)

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

DMS.7: 7 residues within 4Å: Chain A: L.204, V.211, L.213, K.263, L.264, Q.265 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.265

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

PEG.11: 9 residues within 4Å: Chain A: P.68, T.69, F.70, Y.79, K.464, F.465, P.467, H.490, L.532 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.69, A:Y.79, A:Y.79 Water bridges: A:K.464

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

SO4.13: 5 residues within 4Å: Chain A: Y.50, S.51, S.395, W.396, D.397 6 PLIP interactions: 6 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

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

01.14: 13 residues within 4Å: Chain A: L.106, H.404, I.407, T.408, L.411, Y.412, L.475, A.477, N.481, D.482, L.483, D.484, A.485 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.106, A:I.407, A:A.477, A:D.484 Hydrogen bonds: A:L.483, A:A.485 Water bridges: A:N.481

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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