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

Structure of human erythrocyte pyruvate kinase in complex with an allosteric activator Compound 12

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

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.1: 11 residues within 4Å: Chain A: F.39, Y.403, Q.406, L.407, E.410 Chain B: F.39, L.40, L.43, Y.403, Q.406, L.407 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.407, B:L.407 pi-Stacking: A:F.39, A:F.39, B:F.39, B:F.39, B:F.39 I0R.12: 11 residues within 4Å: Chain C: F.39, L.40, L.43, Y.403, Q.406, L.407 Chain D: F.39, Y.403, Q.406, L.407, E.410 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:L.407, C:L.407 pi-Stacking: D:F.39, D:F.39, C:F.39, C:F.39, C:F.39

3 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 9 residues within 4Å: Chain A: R.86, K.283, E.285, A.306, R.307, G.308, D.309, T.341 Ligands: MN.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.308, A:D.309, A:T.341, A:T.341 Salt bridges: A:K.283 PYR.6: 10 residues within 4Å: Chain B: R.86, K.283, E.285, A.306, R.307, G.308, D.309, T.341, M.373 Ligands: MN.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.86, B:G.308, B:D.309, B:T.341 Water bridges: B:S.256 Salt bridges: B:K.283 PYR.9: 11 residues within 4Å: Chain C: R.86, K.283, E.285, M.304, A.306, R.307, G.308, D.309, T.341, M.373 Ligands: MN.11 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.86, C:K.283, C:G.308, C:D.309, C:T.341 Water bridges: C:R.86 Salt bridges: C:K.283

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

FBP.3: 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 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.445, A:T.446, A:T.446, A:T.447, A:G.448, 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, A:R.502, A:G.527 Salt bridges: A:R.502 FBP.7: 19 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, W.528, R.529, P.530, G.531, S.532, G.533, Y.534, T.535 23 PLIP interactions: 23 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:S.532, B:G.533, B:Y.534 Water bridges: B:T.446, B:T.447, B:W.495, B:R.502, B:R.502, B:R.502, B:R.502, B:T.535, B:T.535 Salt bridges: B:R.502 FBP.10: 17 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, R.529, P.530, G.531, S.532, G.533, Y.534, T.535 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:T.445, C:T.446, C:T.446, C:T.447, C:G.448, C:R.449, C:S.450, C:S.450, C:G.527, C:R.529, C:R.529, C:G.531, C:G.533, C:Y.534 Water bridges: C:L.444, C:L.444, C:W.495, C:R.502, C:R.502 Salt bridges: C:R.502 FBP.13: 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 22 PLIP interactions: 22 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:G.531, D:S.532, D:G.533, D:Y.534, D:Y.534 Water bridges: D:W.495, D:R.502, D:R.502, D:R.502, D:R.502, D:G.527, D:T.535, D:T.535 Salt bridges: D:R.502

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

MN.4: 3 residues within 4Å: Chain A: E.285, D.309 Ligands: PYR.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.285, A:D.309, H2O.6 MN.8: 3 residues within 4Å: Chain B: E.285, D.309 Ligands: PYR.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.285, B:D.309, PYR.6 MN.11: 3 residues within 4Å: Chain C: E.285, D.309 Ligands: PYR.9 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.285, C:D.309, H2O.22 MN.14: 2 residues within 4Å: Chain D: E.285, D.309 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.309, D:D.309, H2O.26, H2O.26, H2O.31

2 x K: POTASSIUM ION(Non-covalent)

K.5: 6 residues within 4Å: Chain A: R.86, N.88, S.90, D.126, T.127, K.283 No protein-ligand interaction detected (PLIP) K.15: 1 residues within 4Å: Chain D: N.88 No protein-ligand interaction detected (PLIP)

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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