- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 25 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.2: 5 residues within 4Å:- Chain A: V.87, E.89, R.101, D.103, R.113
Ligand excluded by PLIPEDO.3: 4 residues within 4Å:- Chain A: K.95, D.395, R.398, Q.399
Ligand excluded by PLIPEDO.4: 1 residues within 4Å:- Chain A: Q.876
Ligand excluded by PLIPEDO.5: 5 residues within 4Å:- Chain A: Q.738, K.741, E.742, E.864, L.883
Ligand excluded by PLIPEDO.6: 4 residues within 4Å:- Chain A: Y.260, G.585, G.586, W.587
Ligand excluded by PLIPEDO.9: 7 residues within 4Å:- Chain A: I.763, D.765, Q.766, H.776, Q.787
- Ligands: PGE.7, PEG.8
Ligand excluded by PLIPEDO.11: 4 residues within 4Å:- Chain A: D.720, F.723
- Ligands: PGE.10, PEG.12
Ligand excluded by PLIPEDO.13: 3 residues within 4Å:- Chain A: L.700, D.701
- Ligands: PEG.14
Ligand excluded by PLIPEDO.16: 4 residues within 4Å:- Chain A: R.884, S.897, A.957, D.959
Ligand excluded by PLIPEDO.18: 4 residues within 4Å:- Chain A: R.53, E.293, D.345, S.347
Ligand excluded by PLIPEDO.19: 6 residues within 4Å:- Chain A: K.290, V.291, T.292, E.296, Y.298, P.313
Ligand excluded by PLIPEDO.22: 6 residues within 4Å:- Chain A: R.836, D.846, P.848, P.907, W.909
- Chain B: D.71
Ligand excluded by PLIPEDO.24: 4 residues within 4Å:- Chain A: H.807, G.808, P.809, Q.810
Ligand excluded by PLIPEDO.25: 6 residues within 4Å:- Chain A: Y.733, K.845, L.867, D.868, D.869, G.870
Ligand excluded by PLIPEDO.26: 4 residues within 4Å:- Chain A: S.517, D.518, Y.519, E.520
Ligand excluded by PLIPEDO.27: 2 residues within 4Å:- Chain A: R.631, F.632
Ligand excluded by PLIPEDO.29: 5 residues within 4Å:- Chain A: D.285, S.286, N.311, I.649, E.764
Ligand excluded by PLIPEDO.30: 4 residues within 4Å:- Chain A: A.61, L.62, L.63, D.64
Ligand excluded by PLIPEDO.31: 6 residues within 4Å:- Chain A: F.731, T.734, I.830, P.832, G.863, E.864
Ligand excluded by PLIPEDO.32: 6 residues within 4Å:- Chain A: E.275, H.276, V.277, R.288, L.289, V.291
Ligand excluded by PLIPEDO.33: 5 residues within 4Å:- Chain A: Y.798, K.805, S.856, P.857, G.917
Ligand excluded by PLIPEDO.34: 6 residues within 4Å:- Chain A: R.878, H.879, E.880, K.901, G.902, H.903
Ligand excluded by PLIPEDO.35: 2 residues within 4Å:- Chain A: D.426, A.428
Ligand excluded by PLIPEDO.36: 6 residues within 4Å:- Chain A: A.642, W.644, N.675, P.676, E.677, L.680
Ligand excluded by PLIPEDO.46: 4 residues within 4Å:- Chain B: P.82, S.91, F.92, H.93
Ligand excluded by PLIP- 8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.8: 4 residues within 4Å:- Chain A: S.759, Y.789
- Ligands: PGE.7, EDO.9
No protein-ligand interaction detected (PLIP)PEG.12: 6 residues within 4Å:- Chain A: D.720, F.723, Q.724, S.727, M.835
- Ligands: EDO.11
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.720, A:Q.724
PEG.14: 6 residues within 4Å:- Chain A: W.522, C.523, W.524, F.570
- Ligands: EDO.13, XOD.37
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:C.523
PEG.15: 6 residues within 4Å:- Chain A: V.894, S.895, Q.927, D.959, W.960, S.961
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.895, A:Q.927
PEG.17: 3 residues within 4Å:- Chain A: F.548, A.555, P.556
No protein-ligand interaction detected (PLIP)PEG.20: 5 residues within 4Å:- Chain A: A.478, S.479, R.481
- Chain B: G.112, T.127
1 PLIP interactions:1 interactions with chain A- Water bridges: A:R.481
PEG.28: 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:H.699
PEG.45: 6 residues within 4Å:- Chain B: N.89, G.90, S.91, Y.103, I.104, L.105
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:Y.103
- 1 x XOD: (1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-[(6-{[2-nitro-4-(pyrimidin-2-yl)phenyl]amino}hexyl)amino]cyclohexane-1,2,3,4-tetrol(Non-covalent)
XOD.37: 15 residues within 4Å:- Chain A: F.306, W.422, D.450, I.451, I.487, W.524, W.561, D.563, F.570, R.623, W.636, D.639, F.672, H.697
- Ligands: PEG.14
11 PLIP interactions:11 interactions with chain A- Hydrophobic interactions: A:F.306, A:W.524, A:W.524, A:F.570
- Hydrogen bonds: A:D.450, A:D.450, A:D.563, A:R.623, A:D.639
- Water bridges: A:R.695, A:R.695
- 5 x SO4: SULFATE ION(Non-functional Binders)
SO4.38: 3 residues within 4Å:- Chain A: K.741, D.899
- Ligands: SO4.39
2 PLIP interactions:2 interactions with chain A- Salt bridges: A:K.741, A:H.879
SO4.39: 7 residues within 4Å:- Chain A: Y.737, K.741, Y.875, Q.876, H.879, F.881
- Ligands: SO4.38
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Y.737
- Salt bridges: A:K.741
SO4.40: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)SO4.41: 5 residues within 4Å:- Chain A: W.462, P.468, P.470, E.552, G.553
No protein-ligand interaction detected (PLIP)SO4.47: 7 residues within 4Å:- Chain B: E.122, Y.123, N.124, S.125, G.126, T.127, V.128
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:S.125, B:G.126, B:T.127
- 2 x CA: CALCIUM ION(Non-covalent)
CA.42: 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.43: 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
- 2021-10-06
- Peptides
- Isoform 2 of Neutral alpha-glucosidase AB: A
Glucosidase 2 subunit beta: B - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 25 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 1 x XOD: (1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-[(6-{[2-nitro-4-(pyrimidin-2-yl)phenyl]amino}hexyl)amino]cyclohexane-1,2,3,4-tetrol(Non-covalent)
- 5 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
- 2021-10-06
- Peptides
- Isoform 2 of Neutral alpha-glucosidase AB: A
Glucosidase 2 subunit beta: B - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B