SMTL ID : 7kad.2 (1 other biounit)

Co-crystal structure of alpha glucosidase with compound 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

hetero-1-1-mer

Ligands

1 x W9Y: (1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-[(6-{[2-nitro-4-(1H-1,2,3-triazol-1-yl)phenyl]amino}hexyl)amino]cyclohexane-1,2,3,4-tetrol(Non-covalent)

W9Y.1: 16 residues within 4Å: Chain A: F.306, W.422, D.450, I.451, I.487, W.522, W.524, W.561, D.563, F.570, V.575, R.623, W.636, D.639, F.672, H.697 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.306, A:F.306, A:W.524, A:W.524, A:F.570, A:F.672 Hydrogen bonds: A:D.450, A:D.450, A:D.563, A:D.563, A:R.623, A:D.639 Water bridges: A:D.639, A:R.695 pi-Stacking: A:F.570

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

EDO.2: 8 residues within 4Å: Chain A: N.441, M.442, F.723, V.837, R.838, R.839 Chain B: S.107, R.108 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.107, B:R.108, B:R.108, A:V.837 Water bridges: A:M.442 EDO.3: 3 residues within 4Å: Chain A: R.719, D.720, F.723 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.720, A:D.720 EDO.4: 4 residues within 4Å: Chain A: A.478, S.479, R.481 Chain B: G.112 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.478 EDO.5: 5 residues within 4Å: Chain A: W.462, F.467, P.468, P.470, G.553 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain A: Q.738, K.741, E.742, E.864, L.883 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.738, A:E.742, A:E.742, A:E.864 EDO.9: 6 residues within 4Å: Chain A: F.731, T.734, I.830, P.832, G.863, E.864 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.734, A:T.734, A:E.864 EDO.11: 5 residues within 4Å: Chain A: R.499, W.541, N.544, M.545, N.550 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.499, A:W.541 EDO.12: 2 residues within 4Å: Chain A: T.892, H.963 No protein-ligand interaction detected (PLIP) EDO.13: 2 residues within 4Å: Chain A: R.398, F.744 No protein-ligand interaction detected (PLIP) EDO.14: 3 residues within 4Å: Chain A: R.505, S.517, D.518 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.505, A:D.518, A:D.518 Water bridges: A:D.518, A:E.520 EDO.16: 3 residues within 4Å: Chain A: H.179, R.181, A.182 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.182 EDO.18: 3 residues within 4Å: Chain A: V.925, E.933, R.935 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.933, A:E.933

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

PGE.6: 5 residues within 4Å: Chain A: W.909, K.951, G.953 Chain B: D.70, D.71 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.951

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

PEG.7: 7 residues within 4Å: Chain A: V.894, S.895, Q.927, K.929, D.959, W.960, S.961 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.895 PEG.10: 4 residues within 4Å: Chain A: S.955, A.957, S.958 Ligands: SO4.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.958 PEG.15: 4 residues within 4Å: Chain A: D.439, H.440, N.441, R.719 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.439, A:N.441 PEG.17: 3 residues within 4Å: Chain A: S.762, E.764, D.765 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.762 PEG.19: 2 residues within 4Å: Chain A: G.614, F.873 No protein-ligand interaction detected (PLIP)

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

PG4.20: 6 residues within 4Å: Chain A: M.835, R.912, Q.939 Chain B: C.73, C.75, K.76 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:K.76, B:K.76, A:R.912 Hydrogen bonds: A:Q.939

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

SO4.21: 4 residues within 4Å: Chain A: K.805, H.806, H.807, Q.810 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.807, A:H.807, A:Q.810 Salt bridges: A:K.805 SO4.22: 2 residues within 4Å: Chain A: R.425, R.466 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.466 SO4.23: 9 residues within 4Å: Chain A: L.412, Y.733, W.834, K.845, F.866, L.867, D.868, D.869, G.870 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.868, A:D.868, A:D.868 SO4.24: 6 residues within 4Å: Chain A: K.290, V.291, T.292, E.296, Y.298, P.313 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.291, A:E.296 SO4.25: 5 residues within 4Å: Chain A: T.513, R.514, L.578, D.580, A.581 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.514, A:D.580 SO4.26: 6 residues within 4Å: Chain A: L.904, E.905, T.906, S.955, A.957 Ligands: PEG.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.904, A:T.906, A:S.955, A:S.955 SO4.27: 5 residues within 4Å: Chain A: F.673, K.674, H.699, D.701, T.702 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.674 Salt bridges: A:H.699 SO4.28: 2 residues within 4Å: Chain A: K.674, N.675 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.675, A:N.675

2 x CA: CALCIUM ION(Non-covalent)

CA.29: 6 residues within 4Å: Chain B: Q.67, D.70, Y.72, D.74, D.80, E.81 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:Q.67, B:D.70, B:Y.72, B:D.74, B:D.80, B:E.81 CA.30: 6 residues within 4Å: Chain B: R.108, D.111, V.113, D.115, D.121, E.122 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:R.108, B:D.111, B:V.113, B:D.115, B:D.121, B:E.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karade, S.S. et al., N-Substituted Valiolamine Derivatives as Potent Inhibitors of Endoplasmic Reticulum alpha-Glucosidases I and II with Antiviral Activity. J.Med.Chem. (2021)

Release Date

2021-10-06

Peptides

Isoform 2 of Neutral alpha-glucosidase AB: A
Glucosidase 2 subunit beta: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Isoform 2 of Neutral alpha-glucosidase AB

Glucosidase 2 subunit beta

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