SMTL ID : 9o3b.1 (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: 18 residues within 4Å: Chain A: 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 17 PLIP interactions: 17 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:S.456, A:S.456, A:D.504, A:R.508, A:R.508, A:G.533, A:G.537, A:G.539, A:F.540, A:T.541 Salt bridges: A:R.508 FBP.6: 16 residues within 4Å: Chain B: L.450, T.451, K.452, S.453, 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 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:G.533, B:R.535, B:R.535, B:G.537, B:G.539, B:F.540 Water bridges: B:L.450, B:K.452, B:K.452, B:T.541 Salt bridges: B:K.452, B:R.508

2 x OXL: OXALATE ION(Non-covalent)

OXL.2: 9 residues within 4Å: Chain A: K.289, E.291, M.310, A.312, R.313, G.314, D.315, T.347 Ligands: MG.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.291, A:G.314, A:D.315, A:T.347 Salt bridges: A:R.92, A:K.289 OXL.9: 9 residues within 4Å: Chain C: R.92, K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: MG.12 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.314, C:D.315, C:T.347, C:T.347 Water bridges: C:R.92, C:R.92 Salt bridges: C:R.92, C:K.289, C:K.289

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

EDO.3: 5 residues within 4Å: Chain A: R.62, K.85, S.86, G.87, H.398 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.62 EDO.7: 7 residues within 4Å: Chain B: R.62, N.63, G.65, N.89, H.483, I.488, F.489 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.89, B:I.488 Water bridges: B:G.65 EDO.11: 9 residues within 4Å: Chain C: R.62, N.63, T.64, G.65, N.89, H.483, Y.485, G.487, I.488 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.62, C:H.483, C:H.483, C:G.487

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: E.291, D.315 Ligands: OXL.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.291, A:D.315, H2O.2 MG.8: 3 residues within 4Å: Chain B: S.262, E.291, D.315 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.291, B:D.315, H2O.9 MG.12: 4 residues within 4Å: Chain C: K.289, E.291, D.315 Ligands: OXL.9 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.291, C:D.315, H2O.15 MG.14: 2 residues within 4Å: Chain D: E.291, D.315 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.291, D:D.315

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

01.5: 16 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, N.337, L.372, D.373, Y.409, Q.412, L.413, E.416 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.45, A:L.46, A:Q.412, B:F.45, B:L.413 pi-Stacking: A:F.45, A:F.45, B:F.45 01.10: 16 residues within 4Å: Chain C: F.45, L.46, M.49, L.372, D.373, Y.409, Q.412, L.413 Chain D: F.45, N.337, L.372, D.373, Y.409, Q.412, L.413, E.416 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:L.46, C:Q.412, D:F.45, D:F.45, D:L.413 pi-Stacking: C:F.45, C:F.45, C:F.45, D:F.45

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

PO4.13: 8 residues within 4Å: Chain C: T.451, K.452, S.453, G.454, R.455, S.456, S.538, G.539 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:T.451, C:K.452, C:S.453, C:G.454, C:S.456, C:S.456, C:S.456, C:S.538, C:G.539 Water bridges: C:G.537, C:F.540, C:T.541 PO4.15: 7 residues within 4Å: Chain D: T.451, K.452, S.453, G.454, R.455, S.456, T.541 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.451, D:T.451, D:K.452, D:S.453, D:G.454, D:S.456, D:S.456, D:S.456

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
A

B
B

C
C

D
D

Pyruvate kinase PKM

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