SMTL ID : 4g1n.1

PKM2 in complex with an activator

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x OXL: OXALATE ION(Non-covalent)

OXL.1: 8 residues within 4Å: Chain A: K.257, E.259, A.280, R.281, G.282, D.283, T.315 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.259, A:E.259, A:G.282, A:D.283, A:T.315, A:T.315 Water bridges: A:K.257 Salt bridges: A:R.60, A:K.257, A:K.257 OXL.4: 8 residues within 4Å: Chain B: K.257, E.259, A.280, R.281, G.282, D.283, T.315 Ligands: MG.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.259, B:E.259, B:G.282, B:D.283 Salt bridges: B:R.60, B:K.257 OXL.6: 9 residues within 4Å: Chain C: R.60, K.257, E.259, A.280, R.281, G.282, D.283, T.315 Ligands: MG.7 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:E.259, C:G.282, C:D.283, C:T.315, C:T.315 Water bridges: C:K.257 Salt bridges: C:R.60, C:K.257, C:K.257 OXL.8: 9 residues within 4Å: Chain D: R.60, K.257, E.259, A.280, R.281, G.282, D.283, T.315 Ligands: MG.9 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.282, D:D.283, D:T.315, D:T.315, D:T.315 Water bridges: D:K.257 Salt bridges: D:R.60, D:K.257

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.259, D.283 Ligands: OXL.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.259, A:D.283, H2O.1, H2O.1 MG.5: 3 residues within 4Å: Chain B: E.259, D.283 Ligands: OXL.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.259, B:D.283, H2O.3, H2O.3 MG.7: 4 residues within 4Å: Chain C: K.257, E.259, D.283 Ligands: OXL.6 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.259, C:D.283, H2O.6 MG.9: 3 residues within 4Å: Chain D: E.259, D.283 Ligands: OXL.8 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.259, D:D.283, H2O.8, H2O.8

2 x NZT: N-(4-{[4-(pyrazin-2-yl)piperazin-1-yl]carbonyl}phenyl)quinoline-8-sulfonamide(Non-covalent)

NZT.3: 17 residues within 4Å: Chain A: F.13, M.17, L.340, D.341, I.376, Y.377, Q.380, L.381, E.384 Chain B: F.13, L.14, M.17, K.298, L.340, D.341, Y.377, L.381 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.13, A:F.13, A:L.340, A:L.340, A:Q.380, A:L.381, B:F.13, B:L.14 Hydrogen bonds: A:L.340, A:Y.377 pi-Stacking: A:F.13 NZT.10: 13 residues within 4Å: Chain C: K.298, D.341, L.381, E.384 Chain D: F.13, L.14, M.17, L.340, D.341, I.376, Y.377, Q.380, L.381 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.13, D:F.13, D:L.340, D:L.340, D:Y.377, D:Q.380 Hydrogen bonds: D:L.340, D:Y.377, C:D.341 pi-Stacking: D:F.13 Water bridges: C:K.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kung, C. et al., Small Molecule Activation of PKM2 in Cancer Cells Induces Serine Auxotrophy. Chem.Biol. (2012)

Release Date

2012-10-10

Peptides

Pyruvate kinase isozymes M1/M2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase isozymes M1/M2