- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- hetero-1-1-mer
- 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)
- 13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.2: 6 residues within 4Å:- Chain A: Y.737, Q.738, K.741, E.742, E.864, L.883
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.742
EDO.3: 4 residues within 4Å:- Chain A: R.505, S.517, D.518, E.520
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:D.518, A:D.518, A:E.520
EDO.6: 4 residues within 4Å:- Chain A: R.719, D.720, F.723
- Ligands: PEG.11
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.720, A:D.720
EDO.7: 3 residues within 4Å:- Chain A: F.548, S.554, P.556
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:S.554
EDO.10: 5 residues within 4Å:- Chain A: V.87, E.89, R.101, D.103, R.113
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.113, A:R.113
EDO.12: 2 residues within 4Å:- Chain A: T.406
- Ligands: EDO.21
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:T.406
EDO.13: 6 residues within 4Å:- Chain A: L.904, E.905, T.906, S.955, A.957
- Ligands: PEG.4
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:T.906
EDO.15: 5 residues within 4Å:- Chain A: F.460, R.499, V.500, M.545, N.550
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.499, A:V.500, A:N.550
EDO.16: 6 residues within 4Å:- Chain A: F.731, T.734, I.830, P.832, G.863, E.864
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:T.734, A:T.734, A:E.864
- Water bridges: A:Q.862
EDO.17: 5 residues within 4Å:- Chain A: D.799, S.802, Q.804, H.806, L.814
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:S.802
EDO.21: 5 residues within 4Å:- Chain A: V.119, G.405, T.406, R.631
- Ligands: EDO.12
No protein-ligand interaction detected (PLIP)EDO.24: 4 residues within 4Å:- Chain A: A.478, S.479, R.481
- Chain B: G.112
3 PLIP interactions:3 interactions with chain A- Water bridges: A:S.479, A:R.481, A:R.481
EDO.28: 6 residues within 4Å:- Chain B: E.122, Y.123, N.124, S.125, G.126, T.127
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:E.122, B:S.125, B:G.126, B:T.127
- 6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.4: 4 residues within 4Å:- Chain A: S.955, A.957, S.958
- Ligands: EDO.13
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:S.955, A:S.958
- Water bridges: A:T.928
PEG.8: 7 residues within 4Å:- Chain A: V.894, S.895, Q.927, K.929, D.959, W.960, S.961
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.929, A:D.959
PEG.9: 2 residues within 4Å:- Chain A: G.614, F.873
No protein-ligand interaction detected (PLIP)PEG.11: 4 residues within 4Å:- Chain A: D.439, N.441, R.719
- Ligands: EDO.6
1 PLIP interactions:1 interactions with chain B- Water bridges: B:P.88
PEG.14: 5 residues within 4Å:- Chain A: G.828, T.860, A.861, Q.862, F.888
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:G.828
- Water bridges: A:R.826
PEG.19: 2 residues within 4Å:- Chain A: R.505, N.506
No protein-ligand interaction detected (PLIP)- 2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.5: 6 residues within 4Å:- Chain A: P.907, W.909, K.951, G.953, S.955
- Chain B: D.70
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.951
- Water bridges: A:P.907, A:I.908
PGE.18: 6 residues within 4Å:- Chain A: F.673, K.674, N.675, H.699, D.701, T.702
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.674, A:N.675, A:N.675
- 1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)
- 2 x SO4: SULFATE ION(Non-functional Binders)
SO4.22: 4 residues within 4Å:- Chain A: K.805, H.806, H.807, Q.810
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:H.807, A:Q.810, A:Q.810
- Salt bridges: A:K.805, A:H.806
SO4.23: 8 residues within 4Å:- Chain A: L.412, Y.733, W.834, K.845, L.867, D.868, G.870, I.908
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.868, A:D.868
- 2 x CA: CALCIUM ION(Non-covalent)
CA.25: 6 residues within 4Å:- Chain B: Q.67, D.70, Y.72, D.74, D.80, E.81
6 PLIP interactions:6 interactions with chain B- Metal complexes: B:Q.67, B:D.70, B:Y.72, B:D.74, B:D.80, B:E.81
CA.26: 6 residues within 4Å:- Chain B: R.108, D.111, V.113, D.115, D.121, E.122
6 PLIP interactions:6 interactions with chain B- Metal complexes: B:R.108, B:D.111, B:V.113, B:D.115, B:D.121, B:E.122
- 1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Karade, S.S. et al., N-Substituted Valiolamine Derivatives as Potent Inhibitors of Endoplasmic Reticulum alpha-Glucosidases I and II with Antiviral Activity. J.Med.Chem. (2021)
- Release Date
- 2021-09-29
- Peptides
- Alpha glucosidase 2 alpha neutral subunit: A
Glucosidase 2 subunit beta: B - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- hetero-1-1-mer
- 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)
- 13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)
- 2 x SO4: SULFATE ION(Non-functional Binders)
- 2 x CA: CALCIUM ION(Non-covalent)
- 1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Karade, S.S. et al., N-Substituted Valiolamine Derivatives as Potent Inhibitors of Endoplasmic Reticulum alpha-Glucosidases I and II with Antiviral Activity. J.Med.Chem. (2021)
- Release Date
- 2021-09-29
- Peptides
- Alpha glucosidase 2 alpha neutral subunit: A
Glucosidase 2 subunit beta: B - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
D