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

Co-crystal structure of Chaetomium glucosidase with compound 25

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x W9V: (1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-{[(5Z)-6-{[2-nitro-4-(2H-1,2,3-triazol-2-yl)phenyl]amino}hex-5-en-1-yl]amino}cyclohexane-1,2,3,4-tetrol(Non-covalent)

W9V.1: 15 residues within 4Å: Chain A: P.414, R.421, F.423, W.425, D.426, K.472, P.474, F.477, G.586, D.588, Y.727, W.728, E.785, F.800, W.803 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.425, A:G.586, A:W.728

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: G.171, E.172, N.173, S.174, R.196, S.197, E.198, A.199 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.173, A:R.196, A:E.198, A:A.199 GOL.4: 3 residues within 4Å: Chain A: E.177, G.284, S.285 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.285

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 3 residues within 4Å: Chain A: N.47, R.66, E.444 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.66

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

SO4.5: 3 residues within 4Å: Chain A: G.136, G.137, G.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.137, A:G.311 SO4.6: 6 residues within 4Å: Chain A: S.181, E.182, 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 SO4.7: 5 residues within 4Å: Chain A: G.369, H.370, G.466, A.467, R.470 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.370, A:A.467 Salt bridges: A:H.370, A:R.470 SO4.8: 6 residues within 4Å: Chain A: Y.407, L.452, W.458, I.459, A.460, Q.463 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.452, A:A.460, A:Q.463 SO4.9: 4 residues within 4Å: Chain A: K.341, Y.745, T.749, R.759 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.745 Salt bridges: A:K.341, A:R.759 SO4.10: 4 residues within 4Å: Chain A: T.578, V.579, S.580, H.581 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.578, A:V.579, A:S.580 Salt bridges: A:H.581 SO4.11: 3 residues within 4Å: Chain A: T.315, S.316, K.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.316, A:S.316, A:K.317 SO4.12: 2 residues within 4Å: Chain A: A.467, R.470 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.470

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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