4HDC

Discovery of Selective and Potent Inhibitors of Gram-positive Bacterial Thymidylate Kinase (TMK: Compound 41)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 

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Ligand Structure Quality Assessment 


This is version 1.3 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: SA0440tmk
EC: 2.7.4.9
UniProt
Find proteins for P65249 (Staphylococcus aureus (strain N315))
Explore P65249 
Go to UniProtKB:  P65249
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP65249
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
13Y
Query on 13Y

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-(3-chlorophenoxy)-4-{(1R)-3-methyl-1-[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]butyl}benzoic acid
C28 H32 Cl N3 O5
DUMBOKZAFBZKLT-XUZZJYLKSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
13Y PDBBind:  4HDC IC50: 1.2 (nM) from 1 assay(s)
Binding MOAD:  4HDC IC50: 1.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.53α = 90
b = 90.736β = 101.44
c = 48.346γ = 90
Software Package:
Software NamePurpose
JDirectordata collection
AMoREphasing
BUSTERrefinement
XDSdata reduction
SCALAdata 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
  • Version 1.3: 2024-04-03
    Changes: Refinement description