4QG7

S.aureus TMK in complex with a potent inhibitor compound 18, 2-(3-CHLOROPHENOXY)-3-METHOXY-4-{[(3S)-3-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)PIPERIDIN-1-YL]METHYL}BENZOIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Antibacterial inhibitors of gram-positive thymidylate kinase: structure-activity relationships and chiral preference of a new hydrophobic binding region.

Kawatkar, S.P.Keating, T.A.Olivier, N.B.Breen, J.N.Green, O.M.Guler, S.Y.Hentemann, M.F.Loch, J.T.McKenzie, A.R.Newman, J.V.Otterson, L.G.Martinez-Botella, G.

(2014) J.Med.Chem. 57: 4584-4597

  • DOI: 10.1021/jm500463c
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Thymidylate kinase (TMK), an essential enzyme in bacterial DNA biosynthesis, is an attractive therapeutic target for the development of novel antibacterial agents, and we continue to explore TMK inhibitors with improved potency, protein binding, and ...

    Thymidylate kinase (TMK), an essential enzyme in bacterial DNA biosynthesis, is an attractive therapeutic target for the development of novel antibacterial agents, and we continue to explore TMK inhibitors with improved potency, protein binding, and pharmacokinetic potential. A structure-guided design approach was employed to exploit a previously unexplored region in Staphylococcus aureus TMK via novel interactions. These efforts produced compound 39, with 3 nM IC50 against S. aureus TMK and 2 μg/mL MIC against methicillin-resistant S. aureus (MRSA). This compound exhibits a striking inverted chiral preference for binding relative to earlier compounds and also has improved physical properties and pharmacokinetics over previously published compounds. An example of this new series was efficacious in a murine S. aureus infection model, suggesting that compounds like 39 are options for further work toward a new Gram-positive antibiotic by maintaining a balance of microbiological potency, low clearance, and low protein binding that can result in lower efficacious doses.


    Organizational Affiliation

    Infection Innovative Medicines and ‡Discovery Sciences, AstraZeneca , 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.




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
32K
Query on 32K

Download SDF File 
Download CCD File 
A, B
2-(3-chlorophenoxy)-3-methoxy-4-{[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]methyl}benzoic acid
C25 H26 Cl N3 O6
ZKCQEFJHWRKVMG-SFHVURJKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
32KIC50: 10 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.040α = 90.00
b = 90.450β = 102.10
c = 48.370γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
AMoREphasing
J-Directordata collection
BUSTERrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-05-22 
  • Released Date: 2014-06-11 
  • Deposition Author(s): Olivier, N.B.

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-07-02
    Type: Database references