SMTL ID : 9fb2.1

Gcase in complex with small molecule inhibitor 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.14 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: 6 residues within 4Å: Chain A: R.41, 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.182

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: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.174, A:N.185, A:S.187, H2O.12, H2O.14 K.5: 5 residues within 4Å: Chain A: G.383, 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.16

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

EDO.6: 5 residues within 4Å: Chain A: K.118, W.267, R.316, H.345, M.374 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.345 Water bridges: A:V.117, A:K.118, A:K.118, A:R.316 EDO.7: 4 residues within 4Å: Chain A: R.83, S.84, G.525, Y.526 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.83, A:G.525, A:G.525, A:G.525 EDO.8: 4 residues within 4Å: Chain A: M.400, Q.401, H.404, R.502 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.400 Water bridges: A:R.502, A:R.502, A:R.502 EDO.9: 6 residues within 4Å: Chain A: G.103, L.104, Q.479, V.507, P.508, L.509 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.104, A:P.508 Water bridges: A:Q.479 EDO.10: 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:K.263, A:Q.265 Water bridges: A:L.213

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

PEG.11: 5 residues within 4Å: Chain A: R.41, T.60, Y.61, C.62, L.142 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.41, A:C.62, A:C.62 PEG.12: 11 residues within 4Å: Chain A: P.68, T.69, F.70, Y.79, R.209, K.464, F.465, I.466, P.467, H.490, L.532 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.69, A:Y.79, A:R.209, A:F.465

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

SO4.13: 6 residues within 4Å: Chain A: Y.50, S.51, R.392, S.395, W.396, D.397 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.51, A:S.51, A:S.395, A:W.396, A:D.397, A:D.397 Water bridges: A:R.392, A:R.392, A:S.395, A:S.395 Salt bridges: A:R.392

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

01.14: 14 residues within 4Å: Chain A: L.106, H.404, I.407, T.408, L.411, Y.412, L.475, V.476, A.477, N.481, D.482, L.483, D.484, A.485 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.407, A:L.475, A:A.477, A:D.484 Hydrogen bonds: A:L.483, A:A.485 Water bridges: A:N.481 Salt bridges: A:D.484

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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