› 4jlm

X-ray diffraction
2.18Å resolution

Human dCK C4S-S74E mutant in complex with UDP and the F2.3.1 inhibitor (2-[({5-ETHYL-2-[3-(2-FLUOROETHOXY)-4-METHOXYPHENYL]-1,3-THIAZOL-4-YL}METHYL)SULFANYL]PYRIMIDINE-4,6-DIAMINE)

Released:
DOI: 10.2210/pdb4jlm/pdb
PDB entry 4jlm coloured by chain, front view.
PDB entry 4jlm coloured by chain, side view.
PDB entry 4jlm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural characterization of new deoxycytidine kinase inhibitors rationalizes the affinity-determining moieties of the molecules.
Nomme J, Murphy JM, Su Y, Sansone ND, Armijo AL, Olson ST, Radu C, Lavie A
Acta Crystallogr D Biol Crystallogr 70 68-78 (2014)
PMID: 24419380

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 1NN 3 x 1NN
Ligand UDP 2 x UDP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P41
Unit cell:
a: 68.516Å b: 68.516Å c: 121.285Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.167 0.245
Expression system: Escherichia coli

Quick links

Citations

6 citation in other articles

Co-targeting of convergent nucleotide biosynthetic pathways for leukemia eradication.
Nathanson et al. (2014)
5 more

1 mention without citation

Structural characterization of new deoxycytidine kinase inhibitors rationalizes the affinity-determining moieties of the molecules.
Nomme et al. (2014)