- 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)
- 7 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.2: 4 residues within 4Å:- Chain A: W.909, K.951, G.953
- Chain B: D.70
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:K.951
- Water bridges: B:D.71
PGE.13: 6 residues within 4Å:- Chain A: R.111, Y.112, R.113, Y.584, G.585, W.587
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.111, A:R.113
- Water bridges: A:R.111
PGE.20: 10 residues within 4Å:- Chain A: A.401, S.402, G.405, T.406, H.740, K.741, Y.875, Q.876
- Ligands: EDO.19, SO4.29
1 PLIP interactions:1 interactions with chain A- Water bridges: A:S.402
PGE.21: 9 residues within 4Å:- Chain A: D.438, D.439, H.440, N.441, R.719
- Chain B: L.105, R.108
- Ligands: EDO.22, PGE.33
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:D.438, A:N.441, B:R.108
PGE.24: 6 residues within 4Å:- Chain A: D.455, R.458, T.461, D.495, G.497, Y.498
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.458
- Water bridges: A:W.462
PGE.25: 2 residues within 4Å:- Chain A: S.762, D.765
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:D.765
- Water bridges: A:S.762, A:S.762, A:E.764
PGE.33: 7 residues within 4Å:- Chain B: P.88, N.89, G.90, S.91, Y.103, L.105
- Ligands: PGE.21
No protein-ligand interaction detected (PLIP)- 6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.3: 3 residues within 4Å:- Chain A: S.554, A.555, P.556
No protein-ligand interaction detected (PLIP)PEG.7: 2 residues within 4Å:- Chain A: D.395, R.398
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:S.392, A:D.395
- Water bridges: A:R.398
PEG.8: 2 residues within 4Å:- Chain A: R.132, D.133
No protein-ligand interaction detected (PLIP)PEG.14: 3 residues within 4Å:- Chain A: S.759, Y.789, T.811
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:S.759
- Water bridges: A:S.759, A:Y.789, A:T.811
PEG.15: 6 residues within 4Å:- Chain A: V.894, S.895, Q.927, D.959, W.960, S.961
No protein-ligand interaction detected (PLIP)PEG.16: 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
- Water bridges: A:S.517, A:S.517
- 12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.4: 4 residues within 4Å:- Chain A: Q.738, K.741, E.742, E.864
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Q.738, A:E.864
EDO.5: 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:E.864
- Water bridges: A:I.830, A:Q.862
EDO.6: 4 residues within 4Å:- Chain A: K.95, D.395, R.398, Q.399
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.95, A:Q.399
EDO.9: 3 residues within 4Å:- Chain A: L.63, R.132, V.137
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.132
EDO.10: 2 residues within 4Å:- Chain A: R.537, W.541
No protein-ligand interaction detected (PLIP)EDO.11: 3 residues within 4Å:- Chain A: L.62, L.63, D.64
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:L.63, A:D.64
EDO.12: 5 residues within 4Å:- Chain A: V.87, E.89, R.101, D.103, R.113
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.89, A:R.113, A:R.113
EDO.17: 4 residues within 4Å:- Chain A: Y.798, K.805, S.856, G.917
No protein-ligand interaction detected (PLIP)EDO.18: 2 residues within 4Å:- Chain A: F.873, Q.876
No protein-ligand interaction detected (PLIP)EDO.19: 5 residues within 4Å:- Chain A: V.119, G.405, T.406, R.631
- Ligands: PGE.20
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:T.406, A:T.406
EDO.22: 4 residues within 4Å:- Chain A: R.719, D.720, F.723
- Ligands: PGE.21
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.719
EDO.23: 6 residues within 4Å:- Chain A: K.290, V.291, T.292, E.296, Y.298, P.313
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:E.296, A:E.296
- Water bridges: A:D.285, A:N.311
- 4 x SO4: SULFATE ION(Non-functional Binders)
SO4.26: 2 residues within 4Å:- Chain A: R.466
- Ligands: SO4.27
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:R.466
SO4.27: 2 residues within 4Å:- Chain A: R.425
- Ligands: SO4.26
2 PLIP interactions:2 interactions with chain A- Water bridges: A:N.423, A:R.704
SO4.28: 5 residues within 4Å:- Chain A: K.741, H.879, D.899, K.901
- Ligands: SO4.29
3 PLIP interactions:3 interactions with chain A- Salt bridges: A:K.741, A:H.879, A:K.901
SO4.29: 8 residues within 4Å:- Chain A: Y.737, K.741, Y.875, Q.876, H.879, F.881
- Ligands: PGE.20, SO4.28
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.737
- Salt bridges: A:K.741, A:H.879
- 2 x CA: CALCIUM ION(Non-covalent)
CA.30: 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.31: 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
AB
B
- 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)
- 7 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 4 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
AB
B