SMTL ID : 8e4k.1 (1 other biounit)

Co-crystal structure of Chaetomium glucosidase with compound 7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x UIO: (2R,3R,4R,5S)-2-(hydroxymethyl)-1-[6-({(4M)-4-[2-(morpholin-4-yl)pyrimidin-4-yl]-2-nitrophenyl}amino)hexyl]piperidine-3,4,5-triol(Non-covalent)

UIO.1: 15 residues within 4Å: Chain A: P.414, F.418, F.419, R.421, F.423, W.425, D.426, K.472, G.586, D.588, Y.727, W.728, T.797, F.800, W.803 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.418, A:F.418, A:T.797 Hydrogen bonds: A:W.425, A:W.425 Water bridges: A:N.486, A:E.785 Salt bridges: A:D.426, A:D.588, A:E.785

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: P.541, R.544, R.545 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.544, A:R.544, A:R.545 GOL.3: 7 residues within 4Å: Chain A: R.146, T.208, K.209, G.210, F.301, D.302, S.316 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.208, A:K.209, A:G.210, A:D.302, A:D.302, A:S.316, A:S.316 GOL.4: 7 residues within 4Å: Chain A: G.171, E.172, N.173, S.174, S.197, E.198, A.199 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.173, A:N.173, A:S.174, A:E.198, A:A.199

9 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:A.467 Water bridges: A:E.468 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:V.579, A:S.580, A:H.581 Salt bridges: A:H.581 SO4.7: 3 residues within 4Å: Chain A: Y.745, T.749, R.759 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.745 Salt bridges: A:R.759 SO4.8: 5 residues within 4Å: Chain A: N.496, Y.738, K.809, H.814, H.815 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.809, A:H.815 SO4.9: 6 residues within 4Å: Chain A: Y.407, L.452, W.458, I.459, A.460, Q.463 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.375, A:L.452, A:A.460, A:Q.463 Water bridges: A:Y.407 SO4.10: 7 residues within 4Å: Chain A: S.181, E.182, N.183, G.186, Y.187, E.188, G.189 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.182, A:N.183, A:E.188, A:G.189 SO4.11: 1 residues within 4Å: Chain A: R.470 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.478 Salt bridges: A:R.470 SO4.12: 2 residues within 4Å: Chain A: G.136, G.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.137 SO4.13: 4 residues within 4Å: Chain A: R.544, D.548, D.628, F.631 No protein-ligand interaction detected (PLIP)

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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