› 4qgf

X-ray diffraction
1.83Å resolution

S.aureus TMK in complex with the potent inhibitor compound 38, 2-(3-CHLOROPHENOXY)-3-METHOXY-4-{(1R)-1-[(3S)-3-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)PIPERIDIN-1-YL]PROPYL}BENZOIC ACID

Released:
DOI: 10.2210/pdb4qgf/pdb
PDB entry 4qgf coloured by chain, front view.
PDB entry 4qgf coloured by chain, side view.
PDB entry 4qgf coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus MRSA252
Primary publication:
Antibacterial inhibitors of Gram-positive thymidylate kinase: structure-activity relationships and chiral preference of a new hydrophobic binding region.
Kawatkar SP, Keating TA, Olivier NB, Breen JN, Green OM, Guler SY, Hentemann MF, Loch JT, McKenzie AR, Newman JV, Otterson LG, Martínez-Botella G
J Med Chem 57 4584-97 (2014)
PMID: 24828090

Function and Biology Details

Reaction catalysed: 
ATP + dTMP = ADP + dTDP
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179686 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Thymidylate kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 205 amino acids
Theoretical weight: 23.45 KDa
Source organism: Staphylococcus aureus subsp. aureus MRSA252
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6GJI9 (Residues: 1-205; Coverage: 100%)
Gene names: SAR0483, tmk
Sequence domains: Thymidylate kinase
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

1 bound ligand:
Ligand 32B 2 x 32B
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P21
Unit cell:
a: 46.188Å b: 90.557Å c: 48.448Å
α: 90° β: 101.92° γ: 90°
R-values:
R R work R free
0.169 0.167 0.203
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Genome-scale metabolic models as platforms for identification of novel genes as antimicrobial drug targets.
Mienda et al. (2018)
12 other articles