SMTL ID : 8tbt.1

Structure of human erythrocyte pyruvate kinase in complex with an allosteric activator Compound 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-tetramer

Ligands

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

FBP.1: 18 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, W.528, R.529, P.530, G.531, S.532, G.533, Y.534, T.535 15 PLIP interactions: 15 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:G.531, A:S.532, A:G.533, A:Y.534, A:Y.534 Salt bridges: A:R.502 FBP.6: 17 residues within 4Å: Chain B: L.444, T.445, T.446, T.447, 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 B Hydrogen bonds: B:T.445, B:T.445, B:T.446, B:T.446, B:T.447, B:G.448, B:R.449, B:S.450, B:S.450, B:G.527, B:G.531, B:G.533, B:Y.534, B:Y.534 Water bridges: B:W.495, B:D.498 Salt bridges: B:R.502 FBP.10: 16 residues within 4Å: Chain C: 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 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:T.445, C:T.446, C:T.447, C:G.448, C:S.450, C:S.450, C:S.450, C:G.527, C:G.531, C:G.533, C:Y.534 Salt bridges: C:R.502 FBP.15: 16 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, P.530, G.531, S.532, G.533, Y.534, T.535 18 PLIP interactions: 18 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:G.533, D:Y.534 Water bridges: D:T.446, D:T.446, D:R.502, D:R.502, D:T.535 Salt bridges: D:R.502

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 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.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.308, A:D.309, A:T.341, A:T.341 Water bridges: A:K.283 PYR.7: 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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.283, B:G.308, B:D.309 PYR.11: 10 residues within 4Å: Chain C: R.86, K.283, E.285, A.306, R.307, G.308, D.309, T.341, M.373 Ligands: MN.12 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.283, C:G.308, C:D.309, C:T.341 PYR.16: 9 residues within 4Å: Chain D: R.86, K.283, E.285, A.306, R.307, G.308, D.309, T.341 Ligands: MN.17 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.86, D:K.283, D:G.308, D:D.309, D:T.341, D:T.341 Salt bridges: D:K.283

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

MN.3: 4 residues within 4Å: Chain A: K.283, E.285, D.309 Ligands: PYR.2 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.285, A:D.309, H2O.1, PYR.2 MN.8: 3 residues within 4Å: Chain B: E.285, D.309 Ligands: PYR.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.285, B:D.309, H2O.4, H2O.6 MN.12: 3 residues within 4Å: Chain C: E.285, D.309 Ligands: PYR.11 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.285, C:D.309, H2O.8 MN.17: 3 residues within 4Å: Chain D: E.285, D.309 Ligands: PYR.16 4 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: D:E.285, D:D.309, H2O.14, PYR.16

4 x K: POTASSIUM ION(Non-covalent)

K.4: 6 residues within 4Å: Chain A: N.88, S.90, D.126, T.127, S.256, K.283 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.90, A:D.126, A:T.127, H2O.3 K.9: 5 residues within 4Å: Chain B: N.88, S.90, D.126, T.127, S.256 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.90, B:D.126, B:T.127, H2O.6 K.13: 6 residues within 4Å: Chain C: N.88, S.90, D.126, T.127, S.256, K.283 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.90, C:D.126, C:T.127 K.18: 6 residues within 4Å: Chain D: N.88, S.90, D.126, T.127, S.256, K.283 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.90, D:D.126, D:T.127, H2O.13

2 x I07: {6-[(3-methoxyphenyl)methyl]-4-methyl-5-oxo-5,6-dihydro-4H-thieno[2',3':4,5]pyrrolo[2,3-d]pyridazin-2-yl}(methyl)sulfaniumolate(Non-covalent)

I07.5: 14 residues within 4Å: Chain A: F.39, L.40, L.43, V.402, Y.403, Q.406, L.407 Chain B: F.39, N.331, D.367, Y.403, Q.406, L.407, E.410 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.40, A:L.40, B:L.407 Hydrogen bonds: A:Y.403 pi-Stacking: A:F.39, A:F.39, A:F.39, B:F.39, B:F.39 I07.14: 14 residues within 4Å: Chain C: F.39, L.40, L.43, V.402, Y.403, Q.406, L.407 Chain D: F.39, N.331, D.367, Y.403, Q.406, L.407, E.410 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:F.39, C:L.40, D:L.407 Hydrogen bonds: C:Y.403 pi-Stacking: C:F.39, C:F.39, C:F.39, D:F.39, D: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
A

B
B

C
C

D
D

Pyruvate kinase PKLR

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