› 4q1b

X-ray diffraction
2.15Å resolution

Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 7 {N-(2-(3-(4-(((4,6-diaminopyrimidin-2-yl)thio)methyl)-5-propylthiazol-2-yl)phenoxy)ethyl)methanesulfonamide}

Released:
DOI: 10.2210/pdb4q1b/pdb
PDB entry 4q1b coloured by chain, front view.
PDB entry 4q1b coloured by chain, side view.
PDB entry 4q1b coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-guided development of deoxycytidine kinase inhibitors with nanomolar affinity and improved metabolic stability.
Nomme J, Li Z, Gipson RM, Wang J, Armijo AL, Le T, Poddar S, Smith T, Santarsiero BD, Nguyen HA, Czernin J, Alexandrova AN, Jung ME, Radu CG, Lavie A
OpenAccess logo J Med Chem 57 9480-94 (2014)
PMID: 25341194

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 BL21(DE3)
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 2Y0 2 x 2Y0
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: 68.968Å b: 68.968Å c: 121.944Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.173 0.253
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Re-Discovery of Pyrimidine Salvage as Target in Cancer Therapy.
Walter et al. (2022)
10 other articles

1 mention without citation

Structure-guided development of deoxycytidine kinase inhibitors with nanomolar affinity and improved metabolic stability.
Nomme et al. (2014)