SMTL ID : 9o3b.2 (1 other biounit)

PKM2 bound to MCTI-566

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-tetramer

Ligands

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

FBP.1: 17 residues within 4Å: Chain A: L.450, T.451, K.452, S.453, G.454, R.455, S.456, W.501, R.508, G.533, R.535, P.536, G.537, S.538, G.539, F.540, T.541 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:T.451, A:T.451, A:K.452, A:S.453, A:G.454, A:S.456, A:G.533, A:R.535, A:R.535, A:G.537, A:S.538, A:G.539, A:F.540, A:T.541 Water bridges: A:L.450, A:R.508, A:R.508 Salt bridges: A:K.452, A:R.508 FBP.5: 18 residues within 4Å: Chain B: L.450, T.451, K.452, S.453, R.455, S.456, W.501, D.504, R.508, T.532, G.533, R.535, P.536, G.537, S.538, G.539, F.540, T.541 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:T.451, B:T.451, B:K.452, B:S.453, B:G.454, B:S.456, B:S.456, B:S.456, B:D.504, B:R.508, B:R.508, B:G.533, B:G.537, B:G.539, B:F.540, B:F.540, B:T.541 Water bridges: B:T.451 Salt bridges: B:R.508

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: R.62, N.63, G.65, N.89, H.483, I.488, F.489 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.89, A:I.488 Water bridges: A:G.487 EDO.8: 8 residues within 4Å: Chain C: R.62, N.63, T.64, G.65, N.89, H.483, I.488, F.489 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.483 Water bridges: C:G.65, C:I.488 EDO.13: 11 residues within 4Å: Chain D: R.62, N.63, T.64, G.65, N.89, H.483, Y.485, R.486, G.487, I.488, F.489 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.483, D:Y.485

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: E.291, D.315 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.291, A:D.315, H2O.1, H2O.2 MG.7: 3 residues within 4Å: Chain B: E.291, D.315 Ligands: OXL.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.291, B:D.315, H2O.10 MG.9: 5 residues within 4Å: Chain C: K.134, S.262, K.289, E.291, D.315 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain D: K.289, E.291, D.315 Ligands: OXL.11 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.291, D:D.315, H2O.19

2 x 01: 7-[(dimethylamino)methyl]-8-fluoro-5-methyl-3-[(6-methylpyridin-2-yl)methyl]-3,5-dihydro-4H-pyridazino[4,5-b]indol-4-one

01.4: 17 residues within 4Å: Chain A: F.45, L.46, M.49, L.372, D.373, Y.409, Q.412, L.413 Chain B: F.45, M.49, N.337, L.372, D.373, Y.409, Q.412, L.413, E.416 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.45, B:F.45, B:L.413, A:L.46, A:L.46 pi-Stacking: B:F.45, A:F.45, A:F.45, A:F.45 01.12: 19 residues within 4Å: Chain C: F.45, L.46, M.49, L.372, D.373, Y.409, Q.412, L.413, E.416 Chain D: F.45, L.46, M.49, N.337, L.372, D.373, Y.409, Q.412, L.413, E.416 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.45, D:F.45, D:L.413 pi-Stacking: D:F.45, C:F.45, C:F.45, C:F.45

2 x OXL: OXALATE ION(Non-covalent)

OXL.6: 9 residues within 4Å: Chain B: K.289, E.291, M.310, A.312, R.313, G.314, D.315, T.347 Ligands: MG.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.291, B:G.314, B:D.315, B:T.347 Water bridges: B:R.92, B:R.92, B:K.289 Salt bridges: B:R.92, B:K.289 OXL.11: 9 residues within 4Å: Chain D: K.289, E.291, M.310, A.312, R.313, G.314, D.315, T.347 Ligands: MG.14 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.314, D:D.315, D:T.347, D:T.347 Water bridges: D:S.381 Salt bridges: D:R.92, D:K.289

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.10: 7 residues within 4Å: Chain C: T.451, K.452, S.453, G.454, R.455, S.456, T.541 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.451, C:T.451, C:K.452, C:S.453, C:S.453, C:G.454, C:S.456, C:S.456 PO4.15: 9 residues within 4Å: Chain D: T.451, K.452, S.453, G.454, R.455, S.456, S.538, G.539, T.541 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:T.451, D:T.451, D:K.452, D:S.453, D:S.453, D:S.453, D:G.454, D:S.456, D:S.456, D:G.539, D:T.541 Water bridges: D:F.540, D:T.541

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, W.W. et al., A Novel, Long-Acting, Small Molecule PKM2 Activator and Its Potential Broad Application Against Photoreceptor Degeneration. Transl Vis Sci Technol (2025)

Release Date

2025-08-13

Peptides

Pyruvate kinase PKM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Pyruvate kinase PKM

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