SMTL ID : 8e4z.1 (1 other biounit)

Co-crystal structure of Chaetomium glucosidase with compound 8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

monomer

Ligands

1 x UKF: (2R,3R,4R,5S)-1-(6-{[(4P)-4-(5-cyclobutyl-1,2,4-oxadiazol-3-yl)-2-nitrophenyl]amino}hexyl)-2-(hydroxymethyl)piperidine-3,4,5-triol(Non-covalent)

UKF.1: 15 residues within 4Å: Chain A: Q.96, P.414, F.418, F.419, R.421, F.423, W.425, D.426, G.586, D.588, Y.727, W.728, T.797, F.800, W.803 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.418, A:F.419 Hydrogen bonds: A:F.418, A:W.425, A:W.425, A:D.426, A:W.728 Water bridges: A:N.486 Salt bridges: A:D.426, A:D.588, A:E.785

2 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:P.541, A:R.544, A:R.545 GOL.3: 3 residues within 4Å: Chain A: D.644, S.689, K.691 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.691, A:K.691

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

SO4.4: 5 residues within 4Å: Chain A: G.171, E.172, N.173, S.174, E.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.172, A:N.173, A:E.198 SO4.5: 5 residues within 4Å: Chain A: G.369, H.370, G.466, A.467, R.470 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.370, A:A.467 Water bridges: A:Y.368, A:E.468 Salt bridges: A:H.370, A:R.470 SO4.6: 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 SO4.7: 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 SO4.8: 5 residues within 4Å: Chain A: 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: 5 residues within 4Å: Chain A: N.496, Y.738, K.809, H.814, H.815 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.496 Water bridges: A:K.809 Salt bridges: A:K.809, A:H.815 SO4.10: 4 residues within 4Å: Chain A: T.578, V.579, S.580, H.581 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.578, A:V.579, A:S.580, A:H.581 Water bridges: A:H.581, A:H.581 Salt bridges: A:H.581 SO4.11: 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

Related Entries With Identical Sequence