SMTL ID : 7jty.1 (1 other biounit)

Co-crystal structure of alpha glucosidase with compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

hetero-1-1-mer

Ligands

1 x VND: (1S,2S,3R,4S,5S)-5-(butylamino)-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol(Non-covalent)

VND.1: 16 residues within 4Å: Chain A: F.306, W.422, D.450, I.451, I.487, W.524, W.561, D.563, M.564, R.623, W.636, D.639, F.672, H.697, H.699 Ligands: EDO.6 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.306, A:W.422, A:W.524, A:W.524 Hydrogen bonds: A:D.450, A:D.563, A:R.623, A:D.639, A:H.697, A:H.697 Water bridges: A:G.638, A:D.639

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

SO4.2: 1 residues within 4Å: Chain A: R.466 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.466 SO4.3: 6 residues within 4Å: Chain A: R.878, H.879, E.880, K.901, G.902, H.903 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.878, A:H.903 Water bridges: A:H.879 Salt bridges: A:H.903

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

EDO.4: 7 residues within 4Å: Chain A: A.642, E.643, W.644, N.675, P.676, E.677, L.680 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.643, A:E.677 EDO.5: 4 residues within 4Å: Chain A: D.780, A.781, G.782, A.783 No protein-ligand interaction detected (PLIP) EDO.6: 6 residues within 4Å: Chain A: D.304, F.306, M.564, F.570, R.623 Ligands: VND.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.623 Water bridges: A:D.304, A:F.306 EDO.10: 5 residues within 4Å: Chain A: A.478, S.479, R.481 Chain B: G.112, T.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.481 Water bridges: A:R.481

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

PEG.7: 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

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 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.9: 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

2021-10-13

Peptides

Alpha glucosidase 2 alpha neutral subunit: A
Glucosidase 2 subunit beta: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha glucosidase 2 alpha neutral subunit

Glucosidase 2 subunit beta

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