4HLC

Sulfonylpiperidines as Novel, Antibacterial Inhibitors of Gram-Positive Thymidylate Kinase (TMK): Compound 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Sulfonylpiperidines as novel, antibacterial inhibitors of Gram-positive thymidylate kinase (TMK).

Martinez-Botella, G.Loch, J.T.Green, O.M.Kawatkar, S.P.Olivier, N.B.Boriack-Sjodin, P.A.Keating, T.A.

(2013) Bioorg.Med.Chem.Lett. 23: 169-173

  • DOI: 10.1016/j.bmcl.2012.10.128
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Thymidylate kinase (TMK) is an essential enzyme for DNA synthesis in bacteria, phosphorylating deoxythymidine monophosphate (dTMP) to deoxythymidine diphosphate (dTDP), and thus is a potential new antibacterial drug target. Previously, we have descri ...

    Thymidylate kinase (TMK) is an essential enzyme for DNA synthesis in bacteria, phosphorylating deoxythymidine monophosphate (dTMP) to deoxythymidine diphosphate (dTDP), and thus is a potential new antibacterial drug target. Previously, we have described the first potent and selective inhibitors of Gram-positive TMK, leading to in vivo validation of the target. Here, a structure-guided design approach based on the initial series led to the discovery of novel sulfonylpiperidine inhibitors of TMK. Formation of hydrogen bonds with Arg48 in Staphylococcus aureus TMK was key to obtaining excellent enzyme affinity, as verified by protein crystallography. Replacement of a methylene linker in the series by a sulfonamide was accomplished with retention of binding conformation. Further optimization of logD yielded phenol derivative 11, a potent inhibitor of TMK showing excellent MICs against a broad spectrum of Gram-positive bacteria and >10(5) selectivity versus the human TMK homologue.


    Organizational Affiliation

    AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, MA 02451, USA. gabriel@sagerx.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate kinase
A, B
205Staphylococcus aureus (strain MRSA252)Mutation(s): 0 
Gene Names: tmk
EC: 2.7.4.9
Find proteins for Q6GJI9 (Staphylococcus aureus (strain MRSA252))
Go to UniProtKB:  Q6GJI9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T05
Query on T05

Download SDF File 
Download CCD File 
A, B
4-{[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]sulfonyl}-2-(3-methylphenoxy)benzoic acid
C24 H25 N3 O7 S
HYOKWKXYBOKTDO-KRWDZBQOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
T05IC50: 174 nM BINDINGMOAD
T05IC50: 174 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.200α = 90.00
b = 90.970β = 102.85
c = 48.330γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
BUSTERrefinement
AMoREphasing
CBASSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references