SMTL ID : 9gtw.1

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with iminosugar compound 3g

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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)

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.2: 6 residues within 4Å: Chain A: P.217, H.223, V.230, N.233, T.235, V.236 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.217

1 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.3: 7 residues within 4Å: Chain A: N.470, E.471, T.472, Q.474, P.475, I.477, D.531 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.531

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

NAG.4: 5 residues within 4Å: Chain A: I.383, Q.386, V.387, N.390, Y.685 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.383, A:Q.386, A:V.387 Hydrogen bonds: A:Q.386, A:Q.386, A:N.390 NAG.5: 2 residues within 4Å: Chain A: N.652, L.680 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.652 Water bridges: A:N.652, A:L.678

1 x 01: (2~{S},3~{S},4~{S},5~{S})-2-heptyl-5-(hydroxymethyl)pyrrolidine-3,4-diol

01.6: 15 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, S.676, L.678 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.376, A:W.481, A:F.649, A:L.650, A:L.678 Hydrogen bonds: A:D.404, A:D.404, A:D.518, A:D.518, A:R.600 Water bridges: A:D.616

5 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.866, A:V.867, A:L.868, A:E.869 Water bridges: A:H.717, A:H.717 Salt bridges: A:H.717 SO4.8: 4 residues within 4Å: Chain A: Q.757, K.760, V.763, T.764 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.764, A:T.764 Salt bridges: A:K.760 SO4.9: 5 residues within 4Å: Chain A: G.770, T.771, A.820, T.848, K.849 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.771, A:T.771, A:K.849 Water bridges: A:A.820 SO4.10: 3 residues within 4Å: Chain A: K.96, R.106, F.159 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.96, A:R.106 SO4.11: 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:E.622

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

CL.12: 2 residues within 4Å: Chain A: T.99, Q.100 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain A: S.566 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: S.736, W.804 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 6 residues within 4Å: Chain A: F.414, R.456, P.457, E.505, F.506, Q.509 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.505, A:E.505, A:Q.509 Water bridges: A:R.456, A:Q.509 GOL.16: 6 residues within 4Å: Chain A: D.91, A.93, Q.124, P.125, W.126, C.127 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.91, A:W.126, A:C.127 Water bridges: A:W.126

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

PGE.17: 5 residues within 4Å: Chain A: V.193, P.194, L.577, T.578, A.604 No protein-ligand interaction detected (PLIP) PGE.18: 5 residues within 4Å: Chain A: E.104, G.107, C.108 Ligands: EDO.28, EDO.32 No protein-ligand interaction detected (PLIP) PGE.19: 2 residues within 4Å: Chain A: Q.838, Q.900 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.839, A:Q.900 PGE.21: 2 residues within 4Å: Chain A: F.525, I.526 No protein-ligand interaction detected (PLIP)

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

PEG.20: 5 residues within 4Å: Chain A: D.170, M.172, T.182, K.184, E.192 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.184

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

EDO.22: 5 residues within 4Å: Chain A: L.355, D.356, V.357, G.359, Y.360 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.360 EDO.23: 1 residues within 4Å: Chain A: F.564 No protein-ligand interaction detected (PLIP) EDO.24: 5 residues within 4Å: Chain A: H.432, G.435, R.436, R.437, T.834 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.435 EDO.25: 2 residues within 4Å: Chain A: N.919, L.948 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.919 Water bridges: A:F.947 EDO.26: 4 residues within 4Å: Chain A: V.740, D.741, H.742 Ligands: EDO.33 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.741, A:D.741, A:H.742 EDO.27: 4 residues within 4Å: Chain A: Q.255, Y.256, M.268, L.269 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.268 EDO.28: 5 residues within 4Å: Chain A: C.82, E.104, C.109, Y.110 Ligands: PGE.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.104, A:Y.110 EDO.29: 2 residues within 4Å: Chain A: W.804 Ligands: EDO.31 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.804 EDO.30: 7 residues within 4Å: Chain A: P.779, I.780, Q.827, G.828, P.840, M.841, A.842 No protein-ligand interaction detected (PLIP) EDO.31: 4 residues within 4Å: Chain A: T.764, W.804, T.806 Ligands: EDO.29 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.806 EDO.32: 7 residues within 4Å: Chain A: R.106, G.107, Y.133, P.134, T.156, P.157 Ligands: PGE.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.133 EDO.33: 4 residues within 4Å: Chain A: A.625, H.742, Q.757 Ligands: EDO.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.742

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

2025-10-01

Peptides

Lysosomal alpha-glucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysosomal alpha-glucosidase

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