SMTL ID : 7r6j.2 (1 other biounit)

Co-crystal structure of Chaetomium glucosidase with compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

monomer

Ligands

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.1: 3 residues within 4Å: Chain A: N.47, R.66, E.408 No protein-ligand interaction detected (PLIP)

1 x 2I7: (2R,3R,4R,5S)-2-(hydroxymethyl)-1-[(3-{[3-methyl-5-(pyrimidin-2-yl)anilino]methyl}phenyl)methyl]piperidine-3,4,5-triol(Non-covalent)

2I7.2: 14 residues within 4Å: Chain A: P.414, F.418, F.419, F.423, W.425, D.426, G.586, D.588, Y.727, W.728, E.785, R.796, F.800, W.803 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.418, A:F.419, A:F.423, A:Y.727 Hydrogen bonds: A:W.425, A:D.426, A:D.588, A:Y.727 Water bridges: A:R.461 Salt bridges: A:D.426, A:D.588, A:E.785

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.3: 5 residues within 4Å: Chain A: L.235, T.236, Y.237, Q.251, Q.252 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.236, A:Q.252 Water bridges: A:S.234, A:S.234, A:T.236, A:Q.252, A:Q.252

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 10 residues within 4Å: Chain A: S.371, R.375, E.404, Y.407, L.452, D.454, W.458, I.459, A.460, Q.463 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.371, A:S.371, A:R.375, A:A.460, A:Q.463, A:Q.463 Water bridges: A:Y.407, A:L.452, A:M.453

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

SO4.5: 5 residues within 4Å: Chain A: G.369, H.370, G.466, A.467, R.470 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.370, A:G.466, A:A.467 Salt bridges: A:H.370, A:R.470 SO4.6: 4 residues within 4Å: Chain A: T.578, V.579, S.580, H.581 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.578, A:T.578, A:V.579, A:S.580 Salt bridges: A:H.581 SO4.7: 3 residues within 4Å: Chain A: W.706, R.764, N.768 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.768 Water bridges: A:W.706 Salt bridges: A:R.764 SO4.8: 7 residues within 4Å: Chain A: S.181, E.182, N.183, G.186, Y.187, E.188, G.189 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.182, A:N.183, A:N.183, A:E.188, A:G.189 Water bridges: A:D.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karade, S.S. et al., Structure-Based Design of Potent Iminosugar Inhibitors of Endoplasmic Reticulum alpha-Glucosidase I with Anti-SARS-CoV-2 Activity. J.Med.Chem. (2023)

Release Date

2022-07-06

Peptides

Chaetomium alpha glucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Chaetomium alpha glucosidase

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