4HLD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

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
  • Structures With Same Primary Citation

  • 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 described the first potent and selective inhibitors of Gram-positive TMK, leading to in vivo validation of the target ...

    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 kinaseA, B205Staphylococcus aureus subsp. aureus MRSA252Mutation(s): 0 
Gene Names: SAR0483tmk
EC: 2.7.4.9
Find proteins for Q6GJI9 (Staphylococcus aureus (strain MRSA252))
Explore Q6GJI9 
Go to UniProtKB:  Q6GJI9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
16T
Query on 16T

Download CCD File 
A, B
1-[(3S)-1-{[3-(3-chlorophenoxy)-4-hydroxyphenyl]sulfonyl}piperidin-3-yl]-5-methylpyrimidine-2,4(1H,3H)-dione
C22 H22 Cl N3 O6 S
IDMZBDJWQBWWLK-INIZCTEOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
16TIC50 :  0.5   nM  PDBBind
16TIC50:  0.5   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.49α = 90
b = 90.498β = 104.05
c = 47.803γ = 90
Software Package:
Software NamePurpose
APEXdata collection
AMoREphasing
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-10-16 
  • Released Date: 2012-10-31 
  • Deposition Author(s): Olivier, N.

Revision History 

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