SMTL ID : 9fa6.1

Gcase in complex with small molecule inhibitor 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 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:A.97

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.4, H2O.10, 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.8

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 9 PLIP interactions: 9 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, A:S.395, A:S.395 Salt bridges: A:R.392

2 x 01: ~{N}-[(2~{S})-3-azanyl-2-oxidanyl-propyl]-2-fluoranyl-benzenesulfonamide

01.7: 14 residues within 4Å: Chain A: D.166, F.167, W.218, N.273, E.274, F.285, Y.352, E.379, C.381, S.384, W.420, N.435, F.436, V.437 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:N.435, A:V.437 Hydrogen bonds: A:D.166, A:D.166, A:E.274 Halogen bonds: A:Y.352 01.9: 11 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, L.532 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.68, A:F.70, A:F.465 Hydrogen bonds: A:E.150, A:R.209, A:K.464 Water bridges: A:H.490 Halogen bonds: A:K.464

1 x 02: ~{N}-[(2~{R})-3-azanyl-2-oxidanyl-propyl]-2-fluoranyl-benzenesulfonamide

02.8: 10 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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.411 Hydrogen bonds: A:N.481, A:L.483, A:D.484, A:D.484, A:A.485 Water bridges: A:N.481, A:R.502

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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