- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.35 Å
- Oligo State
- homo-tetramer
- Ligands
- 3 x PYR: PYRUVIC ACID(Non-covalent)
- 4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)
FBP.2: 16 residues within 4Å:- Chain A: L.444, T.445, T.446, T.447, R.449, S.450, W.495, R.502, G.527, R.529, P.530, G.531, S.532, G.533, Y.534, T.535
13 PLIP interactions:13 interactions with chain A- Hydrogen bonds: A:T.445, A:T.446, A:T.447, A:G.448, A:R.449, A:S.450, A:S.450, A:G.527, A:R.529, A:G.531, A:G.533, A:Y.534
- Salt bridges: A:R.502
FBP.6: 16 residues within 4Å:- Chain B: L.444, T.445, T.446, T.447, R.449, S.450, W.495, R.502, G.527, R.529, P.530, G.531, S.532, G.533, Y.534, T.535
21 PLIP interactions:21 interactions with chain B- Hydrogen bonds: B:T.445, B:T.446, B:T.447, B:G.448, B:R.449, B:S.450, B:S.450, B:G.527, B:R.529, B:G.531, B:G.533, B:Y.534
- Water bridges: B:T.446, B:T.446, B:R.468, B:R.502, B:R.502, B:R.502, B:G.527, B:T.535
- Salt bridges: B:R.502
FBP.9: 18 residues within 4Å:- Chain C: L.444, T.445, T.446, T.447, G.448, R.449, S.450, W.495, R.502, G.527, W.528, R.529, P.530, G.531, S.532, G.533, Y.534, T.535
17 PLIP interactions:17 interactions with chain C- Hydrogen bonds: C:T.445, C:T.446, C:T.447, C:G.448, C:R.449, C:S.450, C:S.450, C:G.527, C:G.527, C:R.529, C:G.531, C:S.532, C:G.533, C:Y.534
- Water bridges: C:R.502, C:R.502
- Salt bridges: C:R.502
FBP.12: 15 residues within 4Å:- Chain D: L.444, T.445, T.446, T.447, R.449, S.450, W.495, R.502, G.527, R.529, G.531, S.532, G.533, Y.534, T.535
23 PLIP interactions:23 interactions with chain D- Hydrogen bonds: D:T.445, D:T.446, D:T.446, D:T.447, D:G.448, D:R.449, D:S.450, D:S.450, D:G.527, D:R.529, D:G.531, D:S.532, D:G.533, D:Y.534
- Water bridges: D:R.468, D:R.468, D:W.495, D:R.502, D:R.502, D:R.502, D:R.502, D:G.527
- Salt bridges: D:R.502
- 4 x MN: MANGANESE (II) ION(Non-covalent)
MN.3: 4 residues within 4Å:- Chain A: F.257, E.285, D.309
- Ligands: PYR.1
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Ligand interactions- Metal complexes: A:E.285, A:D.309, PYR.1
MN.7: 3 residues within 4Å:- Chain B: E.285, D.309
- Ligands: PYR.5
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Ligand interactions- Metal complexes: B:E.285, B:D.309, PYR.5
MN.10: 4 residues within 4Å:- Chain C: K.283, E.285, D.309
- Ligands: PYR.8
1 PLIP interactions:1 interactions with chain C- Metal complexes: C:D.309
MN.13: 2 residues within 4Å:- Chain D: E.285, D.309
2 PLIP interactions:1 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:D.309, H2O.23
- 2 x I0R: 6-[(4-hydroxyphenyl)methyl]-2,4-dimethyl-4,6-dihydro-5H-[1,3]thiazolo[5',4':4,5]pyrrolo[2,3-d]pyridazin-5-one(Non-covalent)
I0R.4: 10 residues within 4Å:- Chain A: F.39, L.40, L.43, Y.403, Q.406
- Chain B: F.39, Y.403, Q.406, L.407, E.410
7 PLIP interactions:4 interactions with chain B, 3 interactions with chain A- Hydrophobic interactions: B:L.407
- pi-Stacking: B:F.39, B:F.39, B:F.39, A:F.39, A:F.39, A:F.39
I0R.11: 10 residues within 4Å:- Chain C: F.39, L.40, L.43, Y.403, Q.406
- Chain D: F.39, Y.403, Q.406, L.407, E.410
8 PLIP interactions:5 interactions with chain D, 3 interactions with chain C- Hydrophobic interactions: D:L.407, D:L.407, D:L.407
- pi-Stacking: D:F.39, D:F.39, C:F.39, C:F.39, C:F.39
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Liu, T. et al., Structure-Based Design of AG-946, a Pyruvate Kinase Activator. Chemmedchem (2024)
- Release Date
- 2023-12-27
- Peptides
- Pyruvate kinase PKLR: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
EB
FC
GD
H
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.35 Å
- Oligo State
- homo-tetramer
- Ligands
- 3 x PYR: PYRUVIC ACID(Non-covalent)
- 4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)
- 4 x MN: MANGANESE (II) ION(Non-covalent)
- 2 x I0R: 6-[(4-hydroxyphenyl)methyl]-2,4-dimethyl-4,6-dihydro-5H-[1,3]thiazolo[5',4':4,5]pyrrolo[2,3-d]pyridazin-5-one(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Liu, T. et al., Structure-Based Design of AG-946, a Pyruvate Kinase Activator. Chemmedchem (2024)
- Release Date
- 2023-12-27
- Peptides
- Pyruvate kinase PKLR: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
EB
FC
GD
H