SMTL ID : 7kad.1 (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: 15 residues within 4Å: Chain A: F.306, W.422, D.450, I.451, I.487, W.524, W.561, D.563, F.570, R.623, W.636, D.639, F.672, H.697 Ligands: EDO.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.306, A:F.570 Hydrogen bonds: A:D.450, A:D.450, A:D.563, A:R.623, A:D.639

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

EDO.2: 2 residues within 4Å: Chain A: W.522 Ligands: W9Y.1 Ligand excluded by PLIP EDO.3: 2 residues within 4Å: Chain A: M.835, R.912 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: L.700, D.701 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: K.95, D.395, R.398, Q.399 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: A.478, S.479, R.481 Chain B: G.112 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: V.291, T.292, G.295, E.296, Y.298, P.313 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: H.507, R.537, W.541 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: W.541, N.544, M.545, N.550 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: Q.307, F.673 Ligands: EDO.21 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: I.763, D.765, Q.766, H.776, Q.787 Ligands: PGE.16, PEG.17 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain A: E.161, S.164 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: F.673, K.674, H.699, D.701, T.702 Ligands: EDO.15 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: V.87, E.89, R.101, D.103, R.113 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain A: F.460, T.461, R.499, V.500, N.550 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain A: D.426, E.427, A.428, R.466, P.468 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain A: T.860, A.861, F.888 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain A: I.52, P.58, Y.59, H.79, M.175 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain A: E.679, R.683, G.782, A.783, T.817, L.818 Ligand excluded by PLIP EDO.38: 2 residues within 4Å: Chain B: C.73, C.75 Ligand excluded by PLIP EDO.39: 6 residues within 4Å: Chain B: E.122, Y.123, N.124, S.125, G.126, T.127 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain B: S.91, Y.103, L.105 Ligand excluded by PLIP

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

PGE.4: 6 residues within 4Å: Chain A: R.111, Y.112, R.113, P.115, Y.584, W.587 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.113 Water bridges: A:Y.112 PGE.5: 4 residues within 4Å: Chain A: W.909, K.951, G.953 Chain B: D.70 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.951 PGE.7: 5 residues within 4Å: Chain A: F.394, R.398, E.742, F.744, Q.753 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.398, A:Q.753 PGE.16: 4 residues within 4Å: Chain A: S.762, E.764, D.765 Ligands: EDO.18 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.764 PGE.26: 4 residues within 4Å: Chain A: D.439, N.441, R.719 Ligands: SO4.35 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.439

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

PEG.9: 2 residues within 4Å: Chain A: A.555, P.556 No protein-ligand interaction detected (PLIP) PEG.14: 6 residues within 4Å: Chain A: V.894, S.895, Q.927, D.959, W.960, S.961 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.960, A:S.961 PEG.17: 4 residues within 4Å: Chain A: S.759, Y.789, T.811 Ligands: EDO.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.811, A:T.811 PEG.19: 6 residues within 4Å: Chain A: T.928, K.929, G.930, S.931, P.932, E.933 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.930, A:E.933 PEG.23: 7 residues within 4Å: Chain A: K.483, P.556, Y.559, E.616, D.842, K.845, H.871 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.556, A:Y.559, A:K.845, A:K.845 PEG.24: 6 residues within 4Å: Chain A: R.505, K.512, G.516, S.517, D.518, E.520 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.518, A:D.518 PEG.25: 5 residues within 4Å: Chain A: A.642, W.644, E.677, E.679, L.680 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.677 PEG.28: 4 residues within 4Å: Chain A: G.614, F.873, Q.876, T.877 No protein-ligand interaction detected (PLIP)

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

SO4.33: 3 residues within 4Å: Chain A: H.179, R.181, A.182 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.180, A:A.182 Salt bridges: A:H.179 SO4.34: 3 residues within 4Å: Chain A: K.741, D.899, K.901 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.899 Salt bridges: A:K.741, A:K.901 SO4.35: 4 residues within 4Å: Chain A: R.719, D.720, F.723 Ligands: PGE.26 No protein-ligand interaction detected (PLIP) SO4.36: 4 residues within 4Å: Chain A: Y.260, G.585, G.586, W.587 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.260 Water bridges: A:Y.260, A:G.585 SO4.37: 7 residues within 4Å: Chain A: G.666, A.667, D.668, V.669, F.693, F.694, R.695 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.666, A:D.668, A:V.669, A:R.695, A:R.695

2 x CA: CALCIUM ION(Non-covalent)

CA.41: 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 CA.42: 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

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
A

B
B

Isoform 2 of Neutral alpha-glucosidase AB

Glucosidase 2 subunit beta

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