4GSY | pdb_00004gsy

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) 

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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 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

Macromolecule Content 

  • Total Structure Weight: 47.92 kDa 
  • Atom Count: 3,296 
  • Modeled Residue Count: 384 
  • Deposited Residue Count: 410 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thymidylate kinase
A, B
205Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: SA0440, SAR0483, tmk
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
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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

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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