- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.2: 8 residues within 4Å:- Chain A: V.894, S.895, S.896, 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.6: 3 residues within 4Å:- Chain A: A.957, S.958
- Ligands: PGE.8
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:S.958
PEG.11: 10 residues within 4Å:- Chain A: N.441, M.442, P.443, F.723, V.837, R.838, R.839
- Chain B: L.105, S.107, R.108
5 PLIP interactions:4 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:S.107, B:S.107, B:R.108, B:R.108
- Water bridges: A:M.442
PEG.12: 5 residues within 4Å:- Chain A: L.471, F.548, S.554, A.555, P.556
No protein-ligand interaction detected (PLIP)PEG.17: 8 residues within 4Å:- Chain A: F.460, T.461, G.497, Y.498, R.499, V.500, M.545, N.550
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.499, A:N.550
- Water bridges: A:G.497, A:E.552
PEG.19: 4 residues within 4Å:- Chain A: D.439, N.441, R.719
- Ligands: PGE.38
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.439, A:N.441
- 4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.5: 5 residues within 4Å:- Chain A: W.909, K.951, G.953, S.955
- Chain B: D.70
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.951, A:S.955
PGE.8: 6 residues within 4Å:- Chain A: L.904, E.905, T.906, P.907, A.957
- Ligands: PEG.6
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:T.906
PGE.20: 3 residues within 4Å:- Chain A: S.762, E.764, D.765
2 PLIP interactions:2 interactions with chain A- Water bridges: A:E.764, A:D.765
PGE.38: 8 residues within 4Å:- Chain A: N.441
- Chain B: P.88, N.89, G.90, S.91, Y.103, L.105
- Ligands: PEG.19
3 PLIP interactions:1 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:N.441, B:P.88, 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.29: 15 residues within 4Å:- Chain A: F.306, W.422, D.450, I.451, I.487, W.522, W.524, W.561, D.563, F.570, R.623, W.636, D.639, F.672, H.697
13 PLIP interactions:13 interactions with chain A- Hydrophobic interactions: A:F.306, A:W.524, A:F.672
- Hydrogen bonds: A:D.450, A:D.450, A:D.563, A:D.563, A:R.623, A:D.639, A:D.639
- Water bridges: A:D.639, A:R.695
- pi-Stacking: A:F.570
- 1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 5 x SO4: SULFATE ION(Non-functional Binders)
SO4.31: 2 residues within 4Å:- Chain A: R.466
- Ligands: SO4.32
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:R.466
SO4.32: 2 residues within 4Å:- Chain A: R.425
- Ligands: SO4.31
3 PLIP interactions:3 interactions with chain A- Water bridges: A:R.421, A:N.423, A:R.704
SO4.33: 4 residues within 4Å:- Chain A: F.723, S.727, M.835, V.837
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:F.723, A:S.727
SO4.34: 1 residues within 4Å:- Chain A: S.517
No protein-ligand interaction detected (PLIP)SO4.35: 5 residues within 4Å:- Chain A: W.462, P.468, P.470, E.552, G.553
1 PLIP interactions:1 interactions with chain A- Water bridges: A:L.471
- 2 x CA: CALCIUM ION(Non-covalent)
CA.36: 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.37: 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
- 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
CB
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 4 x PGE: TRIETHYLENE GLYCOL(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)
- 1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 5 x SO4: SULFATE ION(Non-functional Binders)
- 2 x CA: CALCIUM ION(Non-covalent)
- 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
CB
D