› 5eqy

X-ray diffraction
2.5Å resolution

Crystal structure of choline kinase alpha-1 bound by 5-[(4-methyl-1,4-diazepan-1-yl)methyl]-2-[4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]benzenecarbonitrile (compound 65)

Released:
DOI: 10.2210/pdb5eqy/pdb
PDB entry 5eqy coloured by chain, front view.
PDB entry 5eqy coloured by chain, side view.
PDB entry 5eqy coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Novel Small Molecule Inhibitors of Choline Kinase Identified by Fragment-Based Drug Discovery.
Zech SG, Kohlmann A, Zhou T, Li F, Squillace RM, Parillon LE, Greenfield MT, Miller DP, Qi J, Thomas RM, Wang Y, Xu Y, Miret JJ, Shakespeare WC, Zhu X, Dalgarno DC
J Med Chem 59 671-86 (2016)
PMID: 26700752

Function and Biology Details

Reactions catalysed: 
ATP + choline = ADP + phosphocholine
ATP + ethanolamine = ADP + O-phosphoethanolamine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153023 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Choline kinase alpha Chains: A, B
Molecule details ›
Chains: A, B
Length: 401 amino acids
Theoretical weight: 46.86 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P35790 (Residues: 75-457; Coverage: 84%)
Gene names: CHK, CHKA, CKI
Sequence domains: Choline/ethanolamine kinase
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand 5RA 2 x 5RA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU ULTRAX 18
Spacegroup: P212121
Unit cell:
a: 55.523Å b: 121.532Å c: 130.467Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.223 0.277
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Choline Metabolism Alteration: A Focus on Ovarian Cancer.
Bagnoli et al. (2016)
2 more

1 mention without citation

Public Data Set of Protein-Ligand Dissociation Kinetic Constants for Quantitative Structure-Kinetics Relationship Studies.
Liu et al. (2022)