SMTL ID : 4jpg.1

2-((1H-benzo[d]imidazol-1-yl)methyl)-4H-pyrido[1,2-a]pyrimidin-4-ones as Novel PKM2 Activators

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-tetramer

Ligands

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

FBP.1: 17 residues within 4Å: Chain A: L.456, T.457, K.458, S.459, R.461, S.462, W.507, R.514, G.539, W.540, R.541, P.542, G.543, S.544, G.545, F.546, T.547 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.458, A:S.459, A:S.462, A:S.462, A:S.462, A:G.539, A:R.541, A:G.543, A:S.544, A:G.545, A:F.546 Water bridges: A:K.458, A:K.458, A:R.514, A:T.547 Salt bridges: A:K.458, A:R.514 FBP.2: 17 residues within 4Å: Chain B: L.456, T.457, K.458, S.459, G.460, R.461, S.462, W.507, R.514, G.539, R.541, P.542, G.543, S.544, G.545, F.546, T.547 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:K.458, B:S.459, B:G.460, B:S.462, B:S.462, B:G.539, B:R.541, B:R.541, B:G.543, B:S.544, B:G.545, B:F.546, B:T.547 Water bridges: B:R.514, B:R.514, B:T.547 Salt bridges: B:K.458, B:R.514 FBP.4: 18 residues within 4Å: Chain C: L.456, T.457, K.458, S.459, G.460, R.461, S.462, W.507, R.514, T.538, G.539, R.541, P.542, G.543, S.544, G.545, F.546, T.547 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:T.457, C:K.458, C:S.459, C:G.460, C:S.462, C:S.462, C:G.539, C:G.543, C:S.544, C:G.545, C:F.546, C:T.547 Water bridges: C:T.547 Salt bridges: C:R.514 FBP.5: 16 residues within 4Å: Chain D: L.456, T.457, K.458, S.459, R.461, S.462, W.507, R.514, G.539, R.541, P.542, G.543, S.544, G.545, F.546, T.547 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:T.457, D:K.458, D:S.459, D:S.462, D:S.462, D:G.539, D:R.541, D:G.543, D:S.544, D:G.545, D:F.546 Water bridges: D:R.461 Salt bridges: D:K.458, D:R.461, D:R.514

2 x 1OX: 2-(1H-benzimidazol-1-ylmethyl)-4H-pyrido[1,2-a]pyrimidin-4-one(Non-covalent)

1OX.3: 8 residues within 4Å: Chain A: F.51, H.54, L.378, A.413, Y.415 Chain B: F.51, K.336, Q.418 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:K.336, A:L.378, A:L.378 Water bridges: B:K.336, B:D.379 pi-Stacking: B:F.51, B:F.51, A:F.51, A:F.51, A:F.51, A:F.51 1OX.6: 9 residues within 4Å: Chain C: F.51, H.54, L.378, A.413, Y.415, Q.418 Chain D: F.51, K.336, Q.418 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:K.336, C:L.378 Water bridges: D:K.336, D:K.336 pi-Stacking: D:F.51, D:F.51, C:F.51, C:F.51, C:F.51, C:F.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, C. et al., Discovery of 2-((1H-benzo[d]imidazol-1-yl)methyl)-4H-pyrido[1,2-a]pyrimidin-4-ones as novel PKM2 activators. Bioorg.Med.Chem.Lett. (2013)

Release Date

2013-05-22

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