SMTL ID : 8ecw.1 (1 other biounit)

Co-crystal structure of Chaetomium glucosidase with compound 11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x X5B: (2R,3R,4R,5S)-1-{2-[4-(2-{[(5M)-3-chloro-5-(pyridazin-3-yl)phenyl]amino}ethyl)phenyl]ethyl}-2-(hydroxymethyl)piperidine-3,4,5-triol(Non-covalent)

X5B.1: 15 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, T.797, Q.798, F.800 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.418, A:F.418 Hydrogen bonds: A:W.425, A:G.586, A:D.588 Water bridges: A:N.486 Salt bridges: A:D.426, A:E.785 pi-Stacking: A:F.419

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: R.146, T.208, K.209, G.210, E.300, F.301, D.302, S.316 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.146, A:G.210, A:G.210, A:E.300, A:E.300, A:D.302, A:S.316 Water bridges: A:K.209

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

SO4.3: 7 residues within 4Å: Chain A: E.170, G.171, E.172, N.173, S.174, S.197, E.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.173, A:S.174, A:E.198 SO4.4: 3 residues within 4Å: Chain A: G.136, G.137, A.310 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.137 SO4.5: 8 residues within 4Å: Chain A: S.181, E.182, N.183, G.186, Y.187, E.188, G.189, D.190 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.182, A:N.183, A:E.188, A:G.189 SO4.6: 3 residues within 4Å: Chain A: R.225, W.259, A.280 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.225 SO4.7: 1 residues within 4Å: Chain A: W.259 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.259 SO4.8: 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:A.467 Water bridges: A:E.468 Salt bridges: A:H.370, A:R.470 SO4.9: 6 residues within 4Å: Chain A: Y.407, L.452, W.458, I.459, A.460, Q.463 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.452, A:A.460, A:Q.463 Water bridges: A:Y.407 SO4.10: 3 residues within 4Å: Chain A: N.496, K.809, H.815 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.496 Salt bridges: A:K.809, A:H.815 SO4.11: 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:S.580, A:H.581 Salt bridges: A:H.581 SO4.12: 2 residues within 4Å: Chain A: Y.745, R.759 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.745 Salt bridges: A:R.759

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

2023-02-22

Peptides

Chaetomium alpha glucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Chaetomium alpha glucosidase

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