4HDC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.

(2012) J.Med.Chem. 55: 10010-10021

  • DOI: 10.1021/jm3011806
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 agen ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate kinase
A, B
205Staphylococcus aureus (strain N315)Mutation(s): 0 
Gene Names: tmk
EC: 2.7.4.9
Find proteins for P65249 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  P65249
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
13Y
Query on 13Y

Download SDF File 
Download CCD File 
A, B
2-(3-chlorophenoxy)-4-{(1R)-3-methyl-1-[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]butyl}benzoic acid
C28 H32 Cl N3 O5
DUMBOKZAFBZKLT-XUZZJYLKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
13YIC50: 1.2 nM BINDINGMOAD
13YIC50: 1.2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.530α = 90.00
b = 90.736β = 101.44
c = 48.346γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
J-Directordata collection
BUSTERrefinement
XDSdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-10-02 
  • Released Date: 2012-10-24 
  • Deposition Author(s): Olivier, N.B.

Revision History 

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