4GFD

Thymidylate kinase (TMK) from S. Aureus in complex with TK-666


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

In Vivo Validation of Thymidylate Kinase (TMK) with a Rationally Designed, Selective Antibacterial Compound.

Keating, T.A.Newman, J.V.Olivier, N.B.Otterson, L.G.Andrews, B.Boriack-Sjodin, P.A.Breen, J.N.Doig, P.Dumas, J.Gangl, E.Green, O.M.Guler, S.Y.Hentemann, M.F.Joseph-McCarthy, D.Kawatkar, S.Kutschke, A.Loch, J.T.McKenzie, A.R.Pradeepan, S.Prasad, S.Martinez-Botella, G.

(2012) Acs Chem.Biol. 7: 1866-1872

  • DOI: 10.1021/cb300316n

  • PubMed Abstract: 
  • There is an urgent need for new antibacterials that pinpoint novel targets and thereby avoid existing resistance mechanisms. We have created novel synthetic antibacterials through structure-based drug design that specifically target bacterial thymidy ...

    There is an urgent need for new antibacterials that pinpoint novel targets and thereby avoid existing resistance mechanisms. We have created novel synthetic antibacterials through structure-based drug design that specifically target bacterial thymidylate kinase (TMK), a nucleotide kinase essential in the DNA synthesis pathway. A high-resolution structure shows compound TK-666 binding partly in the thymidine monophosphate substrate site, but also forming new induced-fit interactions that give picomolar affinity. TK-666 has potent, broad-spectrum Gram-positive microbiological activity (including activity against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus), bactericidal action with rapid killing kinetics, excellent target selectivity over the human ortholog, and low resistance rates. We demonstrate in vivo efficacy against S. aureus in a murine infected-thigh model. This work presents the first validation of TMK as a compelling antibacterial target and provides a rationale for pursuing novel clinical candidates for treating Gram-positive infections through TMK.


    Organizational Affiliation

    AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States. thomas.keating@astrazeneca.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate kinase
A, B
205Staphylococcus aureus (strain Mu50 / ATCC 700699)Mutation(s): 0 
Gene Names: tmk
EC: 2.7.4.9
Find proteins for P65248 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Go to UniProtKB:  P65248
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0YB
Query on 0YB

Download SDF File 
Download CCD File 
A, B
2-(3-bromophenoxy)-4-{(1R)-3,3-dimethyl-1-[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]butyl}benzoic acid
C29 H34 Br N3 O5
SXYGLXXKMZTVNB-XUZZJYLKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0YBKi: 0.33 nM BINDINGMOAD
0YBKi: 0.33 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.100α = 90.00
b = 90.540β = 103.08
c = 48.200γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
StructureStudiodata collection
SCALAdata scaling
BUSTERrefinement
PROCESSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references