SMTL ID : 9gsv.1

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with iminosugar compound 4c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 3 residues within 4Å: Chain A: E.139, N.140, T.153 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA.2: 5 residues within 4Å: Chain A: P.217, V.230, N.233, T.235, V.236 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.217 NAG-NAG-BMA.4: 6 residues within 4Å: Chain A: N.470, T.472, Q.474, P.475, I.477, D.531 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.531

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

NAG-NAG.3: 5 residues within 4Å: Chain A: I.383, Q.386, V.387, N.390, Y.685 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.5: 2 residues within 4Å: Chain A: N.652, L.680 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.680 Hydrogen bonds: A:N.652

1 x 01: (2~{R},3~{R},4~{R},5~{S})-2-(hydroxymethyl)-2-(2-phenylethyl)piperidine-3,4,5-triol

01.6: 14 residues within 4Å: Chain A: W.376, D.404, L.405, I.441, W.481, W.516, D.518, R.600, W.613, D.616, F.649, L.650, H.674 Ligands: PG4.17 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.376, A:W.376, A:W.481, A:F.649, A:F.649, A:L.650 Hydrogen bonds: A:D.518, A:D.518, A:R.600, A:D.616, A:H.674 Water bridges: A:W.481, A:D.518, A:D.616, A:D.616

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

SO4.7: 5 residues within 4Å: Chain A: H.717, E.866, V.867, L.868, E.869 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.866, A:V.867, A:L.868, A:E.869 Salt bridges: A:H.717 SO4.8: 4 residues within 4Å: Chain A: Q.757, K.760, V.763, T.764 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.764 Salt bridges: A:K.760 SO4.9: 3 residues within 4Å: Chain A: S.620, W.621, E.622 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.621, A:E.622 Water bridges: A:S.620, A:S.620

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 3 residues within 4Å: Chain A: R.189, Y.191, S.566 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: S.918, V.939, S.940 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: T.771, K.849 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: Y.360, R.608 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: F.564 Ligand excluded by PLIP

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.15: 6 residues within 4Å: Chain A: R.168, D.170, M.172, T.182, K.184, E.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.184, A:E.192 Water bridges: A:E.192 PGE.16: 5 residues within 4Å: Chain A: I.581, H.584, R.585, R.608, Y.609 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.585, A:R.585, A:R.608

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.17: 5 residues within 4Å: Chain A: D.282, A.284, D.616, L.650 Ligands: 01.6 No protein-ligand interaction detected (PLIP) PG4.18: 3 residues within 4Å: Chain A: Q.838, G.898, Q.900 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.900

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

EDO.19: 3 residues within 4Å: Chain A: V.740, D.741, H.742 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.741, A:D.741, A:H.742 EDO.20: 3 residues within 4Å: Chain A: P.690, A.691, L.811 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.694 EDO.21: 3 residues within 4Å: Chain A: P.840, Q.900, Q.902 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.900 EDO.22: 6 residues within 4Å: Chain A: F.414, R.456, P.457, M.502, E.505, F.506 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.502 EDO.23: 4 residues within 4Å: Chain A: M.173, E.174, T.175, E.176 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.175 EDO.24: 2 residues within 4Å: Chain A: K.96, R.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.96, A:R.106 Water bridges: A:Q.102 EDO.25: 3 residues within 4Å: Chain A: E.869, G.871, Y.873 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.873, A:Y.873 EDO.26: 1 residues within 4Å: Chain A: I.581 No protein-ligand interaction detected (PLIP) EDO.27: 5 residues within 4Å: Chain A: H.432, G.435, R.436, R.437, T.834 No protein-ligand interaction detected (PLIP) EDO.28: 3 residues within 4Å: Chain A: Q.255, Y.256, L.269 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.256, A:L.269

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vieira Da Cruz, A. et al., C -Branched Iminosugars as Selective Pharmacological Chaperones of Lysosomal alpha-Glucosidase for the Treatment of Pompe Disease. J.Med.Chem. (2025)

Release Date

2025-09-24

Peptides

Lysosomal alpha-glucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysosomal alpha-glucosidase

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