› 4hld

X-ray diffraction
2Å resolution

Sulfonylpiperidines as Novel, Antibacterial Inhibitors of Gram-Positive Thymidylate Kinase (TMK): Compound 11

Released:
DOI: 10.2210/pdb4hld/pdb
PDB entry 4hld coloured by chain, front view.
PDB entry 4hld coloured by chain, side view.
PDB entry 4hld coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus MRSA252
Primary publication:
Sulfonylpiperidines as novel, antibacterial inhibitors of Gram-positive thymidylate kinase (TMK).
Martínez-Botella G, Loch JT, Green OM, Kawatkar SP, Olivier NB, Boriack-Sjodin PA, Keating TA
Bioorg Med Chem Lett 23 169-73 (2013)
PMID: 23206863

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 16T 2 x 16T
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P21
Unit cell:
a: 45.49Å b: 90.498Å c: 47.803Å
α: 90° β: 104.05° γ: 90°
R-values:
R R work R free
0.209 0.208 0.239
Expression system: Escherichia coli BL21(DE3)

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Citations

2 review citations

Prospects for new antibiotics: a molecule-centered perspective.
Walsh et al. (2014)
1 more

1 mention without citation

Separation of cordycepin from Cordyceps militaris fermentation supernatant using preparative HPLC and evaluation of its antibacterial activity as an NAD+-dependent DNA ligase inhibitor.
Zhou et al. (2016)