› 4jlk

X-ray diffraction
1.89Å resolution

Human dCK C4S-S74E mutant in complex with UDP and the F2.2.1 inhibitoR (2-[({2-[3-(2-FLUOROETHOXY)-4-METHOXYPHENYL]-5-METHYL-1,3-THIAZOL-4-YL}METHYL)SULFANYL]PYRIMIDINE-4,6-DIAMINE)

Released:
DOI: 10.2210/pdb4jlk/pdb
PDB entry 4jlk coloured by chain, front view.
PDB entry 4jlk coloured by chain, side view.
PDB entry 4jlk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Development of new deoxycytidine kinase inhibitors and noninvasive in vivo evaluation using positron emission tomography.
Murphy JM, Armijo AL, Nomme J, Lee CH, Smith QA, Li Z, Campbell DO, Liao HI, Nathanson DA, Austin WR, Lee JT, Darvish R, Wei L, Wang J, Su Y, Damoiseaux R, Sadeghi S, Phelps ME, Herschman HR, Czernin J, Alexandrova AN, Jung ME, Lavie A, Radu CG
J Med Chem 56 6696-708 (2013)
PMID: 23947754

Function and Biology Details

Reactions catalysed: 
ATP + deoxyguanosine = ADP + dGMP
NTP + deoxycytidine = NDP + dCMP
ATP + deoxyadenosine = ADP + dAMP
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151058 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxycytidine kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 280 amino acids
Theoretical weight: 32.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P27707 (Residues: 1-260; Coverage: 100%)
Gene name: DCK
Sequence domains: Deoxynucleoside kinase
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

2 bound ligands:
Ligand UDP 2 x UDP
Ligand 1NO 4 x 1NO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P41
Unit cell:
a: 68.6Å b: 68.6Å c: 120.706Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.167 0.215
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Radiopharmaceuticals as probes to characterize tumour tissue.
Alam et al. (2015)
14 other articles

2 mentions without citation

Survey of phosphorylation near drug binding sites in the Protein Data Bank (PDB) and their effects.
Smith et al. (2015)
1 more