4GSY

Crystal structure of thymidylate kinase from Staphylococcus aureus bound to inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 
    0.205 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/jm3011806
  • Primary Citation of Related Structures:  
    4GSY, 4HDC, 4HEJ

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thymidylate kinase
A, B
205Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: SA0440SAR0483tmk
EC: 2.7.4.9
UniProt
Find proteins for Q6GJI9 (Staphylococcus aureus (strain MRSA252))
Explore Q6GJI9 
Go to UniProtKB:  Q6GJI9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6GJI9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0Y5
Query on 0Y5

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4-{[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]methyl}-2-[3-(trifluoromethyl)phenoxy]benzoic acid
C25 H24 F3 N3 O5
SLYIQORXPGMWOF-SFHVURJKSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free:  0.205 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.984α = 90
b = 90.635β = 102.99
c = 48.409γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
BUSTERrefinement
autoPROCdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Refinement description