ISDA

Deposition Date 2012-10-02

Release Date 2012-10-24

Last Version Date 2024-04-03

Entry Detail

PDB ID:

4HDC

Keywords:

TRANSFERASE/TRANSFERASE INHIBITOR

Title:

Discovery of Selective and Potent Inhibitors of Gram-positive Bacterial Thymidylate Kinase (TMK: Compound 41)

Biological Source:

Source Organism:

Staphylococcus aureus subsp. aureus (Taxon ID: 158879)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.05 Å

R-Value Free:

0.25

R-Value Work:

0.21

Space Group:

P 1 21 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Thymidylate kinase
Gene (Uniprot):tmk
Chain IDs:A, B
Chain Length:205
Number of Molecules:2
Biological Source:Staphylococcus aureus subsp. aureus

UniProt ID:P65249 Pfam ID:PF02223

Ligand Molecules

13Y

Primary Citation

Discovery of Selective and Potent Inhibitors of Gram-Positive Bacterial Thymidylate Kinase (TMK).

Martinez-Botella, G, Breen, J.N, Duffy, J.E, Dumas, J, Geng, B, Gowers, I.K, Green, O.M, Guler, S, Hentemann, M.F, Hernandez-Juan, F.A, Joseph-McCarthy, D, Kawatkar, S, Larsen, N.A, Lazari, O, Loch, J.T, Macritchie, J.A, McKenzie, A.R, Newman, J.V, Olivier, N.B, Otterson, L.G, Owens, A.P, Read, J, Sheppard, D.W, Keating, T.A.Show

J.Med.Chem. 55 10010 10021 (2012)

PMID: 23043329 DOI: 10.1021/jm3011806

Abstact

Thymidylate kinase (TMK) is an essential enzyme in bacterial DNA synthesis. The deoxythymidine monophosphate (dTMP) substrate binding pocket was targeted in a rational-design, structure-supported effort, yielding a unique series of antibacterial agents showing a novel, induced-fit binding mode. Lead optimization, aided by X-ray crystallography, led to picomolar inhibitors of both Streptococcus pneumoniae and Staphylococcus aureus TMK. MICs < 1 μg/mL were achieved against methicillin-resistant S. aureus (MRSA), S. pneumoniae, and vancomycin-resistant Enterococcus (VRE). Log D adjustments yielded single diastereomers 14 (TK-666) and 46, showing a broad antibacterial spectrum against Gram-positive bacteria and excellent selectivity against the human thymidylate kinase ortholog.

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Primary Citation of related structures