4HEJ | pdb_00004hej

Discovery of Selective and Potent Inhibitors of Gram-positive Bacterial Thymidylate Kinase (TMK): Compund 16

• PDB DOI: https://doi.org/10.2210/pdb4HEJ/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Staphylococcus aureus subsp. aureus N315
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-10-03 Released: 2012-10-24 
• Deposition Author(s): Martinez-Botella, G., Breen, J., Duffy, J., Dumas, J., Geng, B., Gowers, I., Green, O., Guler, S., Hentemann, M., Hernandez-Juan, F., Joseph-McCarthy, D., Kawatkar, S., Larsen, N., Lazari, O., Loch, J., Macritchie, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.235 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

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

• PubMed: 23043329 
• 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.

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Organizational Affiliation: 
• AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.37 kDa 
• Atom Count: 3,384 
• Modeled Residue Count: 395 
• Deposited Residue Count: 410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate kinase	A, B	205	Staphylococcus aureus subsp. aureus N315	Mutation(s): 0  Gene Names: SA0440, tmk EC: 2.7.4.9
UniProt
Find proteins for P65249 (Staphylococcus aureus (strain N315)) Explore P65249  Go to UniProtKB:  P65249

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
14D	C [auth A]	5-methyl-1-[(3S)-1-{3-[3-(trifluoromethyl)phenoxy]benzyl}piperidin-3-yl]pyrimidine-2,4(1H,3H)-dione C24 H24 F3 N3 O3 OVDFDRSJZJQKLN-IBGZPJMESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.235 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.348	α = 90
b = 90.308	β = 100.69
c = 50.07	γ = 90

Software Package:

Software Name	Purpose
JDirector	data collection
AMoRE	phasing
BUSTER	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-24 
Deposition Author(s): Martinez-Botella, G., Breen, J., Duffy, J., Dumas, J., Geng, B., Gowers, I., Green, O., Guler, S., Hentemann, M., Hernandez-Juan, F., Joseph-McCarthy, D., Kawatkar, S., Larsen, N., Lazari, O., Loch, J., Macritchie, J.

Revision History  

• 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