› 4jpg

X-ray diffraction
2.33Å resolution

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

Released:
DOI: 10.2210/pdb4jpg/pdb
PDB entry 4jpg coloured by chain, front view.
PDB entry 4jpg coloured by chain, side view.
PDB entry 4jpg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of 2-((1H-benzo[d]imidazol-1-yl)methyl)-4H-pyrido[1,2-a]pyrimidin-4-ones as novel PKM2 activators.
Guo C, Linton A, Jalaie M, Kephart S, Ornelas M, Pairish M, Greasley S, Richardson P, Maegley K, Hickey M, Li J, Wu X, Ji X, Xie Z
Bioorg Med Chem Lett 23 3358-63 (2013)
PMID: 23622982

Function and Biology Details

Reactions catalysed: 
ATP + pyruvate = ADP + phosphoenolpyruvate
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146985 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyruvate kinase PKM Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 556 amino acids
Theoretical weight: 60.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P14618 (Residues: 1-531; Coverage: 100%)
Gene names: OIP3, PK2, PK3, PKM, PKM2
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand FBP 4 x FBP
Ligand 1OX 2 x 1OX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P21
Unit cell:
a: 80.971Å b: 153.613Å c: 93.479Å
α: 90° β: 103.45° γ: 90°
R-values:
R R work R free
0.18 0.178 0.219
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Pyruvate kinase M2 at a glance.
Yang et al. (2015)
9 more

4 mentions without citation

Aerobic Glycolysis in the Retina: Functional Roles of Pyruvate Kinase Isoforms.
Rajala RVS. (2020)
3 more