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 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

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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
Binding Affinity Annotations 
IDSourceBinding Affinity
0Y5 PDBBind:  4GSY IC50: 120 (nM) from 1 assay(s)
Binding MOAD:  4GSY IC50: 120 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • 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