SMTL ID : 8tbs.1 (1 other biounit)

Structure of human erythrocyte pyruvate kinase in complex with an allosteric activator AG-946

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FBP.1: 17 residues within 4Å: Chain A: L.444, T.445, T.446, T.447, G.448, R.449, S.450, W.495, R.502, G.527, R.529, P.530, G.531, S.532, G.533, Y.534, T.535 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:T.445, A:T.446, 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 Water bridges: A:R.502, A:R.502 Salt bridges: A:R.502 FBP.6: 18 residues within 4Å: Chain B: L.444, T.445, T.446, T.447, G.448, R.449, S.450, W.495, R.502, T.526, G.527, R.529, P.530, G.531, S.532, G.533, Y.534, T.535 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:T.445, B:T.445, B:T.446, B:T.447, B:G.448, B:R.449, B:S.450, B:G.527, B:R.529, B:G.531, B:G.533, B:Y.534 Water bridges: B:L.444, B:L.444, B:T.446, B:R.468, B:R.502, B:R.502, B:R.502, B:T.535, B:T.535 Salt bridges: B:R.502 FBP.10: 18 residues within 4Å: Chain C: L.444, T.445, T.446, T.447, G.448, R.449, S.450, W.495, R.502, T.526, G.527, 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.446, C:T.446, C:T.447, C:T.447, C:T.447, C:G.448, C:R.449, C:S.450, C:G.527, C:G.531, C:G.533, C:Y.534 Water bridges: C:R.502, C:R.502, C:R.502, C:R.502 Salt bridges: C:R.502 FBP.15: 17 residues within 4Å: Chain D: L.444, T.445, T.446, T.447, G.448, R.449, S.450, W.495, R.502, G.527, R.529, P.530, G.531, S.532, G.533, Y.534, T.535 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:T.445, 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:T.535 Salt bridges: D:R.502

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 3 residues within 4Å: Chain A: E.285, D.309 Ligands: PYR.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.285, A:D.309, PYR.4 MN.7: 3 residues within 4Å: Chain B: E.285, D.309 Ligands: PYR.9 5 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:E.285, B:D.309, H2O.4, H2O.4, PYR.9 MN.11: 3 residues within 4Å: Chain C: E.285, D.309 Ligands: PYR.13 4 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: C:E.285, C:D.309, H2O.6, PYR.13 MN.16: 4 residues within 4Å: Chain D: K.283, E.285, D.309 Ligands: PYR.17 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.285, D:D.309, H2O.9

3 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: N.88, S.90, D.126, T.127, S.256, K.283 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.90, A:D.126, A:T.127 K.8: 6 residues within 4Å: Chain B: N.88, S.90, D.126, T.127, S.256, K.283 No protein-ligand interaction detected (PLIP) K.12: 6 residues within 4Å: Chain C: N.88, S.90, D.126, T.127, S.256, K.283 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.90

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.4: 10 residues within 4Å: Chain A: R.86, K.283, E.285, A.306, R.307, G.308, D.309, T.341, M.373 Ligands: MN.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.308, A:D.309, A:T.341, A:T.341 Water bridges: A:R.86 Salt bridges: A:K.283 PYR.9: 8 residues within 4Å: Chain B: K.283, E.285, A.306, R.307, G.308, D.309, T.341 Ligands: MN.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.308, B:D.309 Water bridges: B:K.283 Salt bridges: B:K.283 PYR.13: 9 residues within 4Å: Chain C: K.283, E.285, A.306, R.307, G.308, D.309, T.341, M.373 Ligands: MN.11 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.308, C:D.309, C:T.341 Water bridges: C:K.283 Salt bridges: C:K.283 PYR.17: 9 residues within 4Å: Chain D: R.86, K.283, A.306, R.307, G.308, D.309, T.341, M.373 Ligands: MN.16 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.283, D:G.308, D:D.309 Water bridges: D:R.86

2 x HVI: 6-[(6-aminopyridin-2-yl)methyl]-4-methyl-2-[(1H-pyrazol-3-yl)methyl]-4,6-dihydro-5H-[1,3]thiazolo[5',4':4,5]pyrrolo[2,3-d]pyridazin-5-one(Non-covalent)

HVI.5: 13 residues within 4Å: Chain A: F.39, L.40, Y.403, Q.406, L.407, E.410 Chain B: F.39, L.366, D.367, Y.403, Q.406, L.407, E.410 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.40, A:L.407, A:L.407, B:L.407, B:L.407 Water bridges: A:D.367 pi-Stacking: A:F.39, A:F.39, A:F.39, B:F.39, B:F.39, B:F.39 Hydrogen bonds: B:L.366 HVI.14: 12 residues within 4Å: Chain C: F.39, L.43, Y.403, Q.406, L.407 Chain D: F.39, L.366, D.367, Y.403, Q.406, L.407, E.410 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:L.407, C:L.407, C:L.407 Hydrogen bonds: D:L.366 pi-Stacking: D:F.39, D:F.39, D:F.39, C:F.39, C:F.39, C:F.39 Water bridges: C:D.367

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
A

B
B

C
C

D
D

Pyruvate kinase PKLR

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