Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 47.91 kDa 
• Atom Count: 3518 
• Modelled Residue Count: 392 
• Deposited Residue Count: 410 
• Unique protein chains: 1

4HLC

Sulfonylpiperidines as Novel, Antibacterial Inhibitors of Gram-Positive Thymidylate Kinase (TMK): Compound 5

• DOI: 10.2210/pdb4HLC/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Staphylococcus aureus subsp. aureus MRSA252
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-10-16 Released: 2012-10-31 
• Deposition Author(s): Boriack-Sjodin, A., Olivier, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.199 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Literature

Sulfonylpiperidines as novel, antibacterial inhibitors of Gram-positive thymidylate kinase (TMK).

Martinez-Botella, G., Loch, J.T., Green, O.M., Kawatkar, S.P., Olivier, N.B., Boriack-Sjodin, P.A., Keating, T.A.

(2013) Bioorg Med Chem Lett 23: 169-173

• PubMed: 23206863 
• DOI: 10.1016/j.bmcl.2012.10.128
• Primary Citation of Related Structures:  
  4HLC, 4HLD


• PubMed Abstract: 
  

Thymidylate kinase (TMK) is an essential enzyme for DNA synthesis in bacteria, phosphorylating deoxythymidine monophosphate (dTMP) to deoxythymidine diphosphate (dTDP), and thus is a potential new antibacterial drug target. Previously, we have described the first potent and selective inhibitors of Gram-positive TMK, leading to in vivo validation of the target. Here, a structure-guided design approach based on the initial series led to the discovery of novel sulfonylpiperidine inhibitors of TMK. Formation of hydrogen bonds with Arg48 in Staphylococcus aureus TMK was key to obtaining excellent enzyme affinity, as verified by protein crystallography. Replacement of a methylene linker in the series by a sulfonamide was accomplished with retention of binding conformation. Further optimization of logD yielded phenol derivative 11, a potent inhibitor of TMK showing excellent MICs against a broad spectrum of Gram-positive bacteria and >10(5) selectivity versus the human TMK homologue.

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Organizational Affiliation: 

AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, MA 02451, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate kinase	A, B	205	Staphylococcus aureus subsp. aureus MRSA252	Mutation(s): 0  Gene Names: SAR0483, tmk EC: 2.7.4.9
Find proteins for Q6GJI9 (Staphylococcus aureus (strain MRSA252)) Explore Q6GJI9  Go to UniProtKB:  Q6GJI9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T05	C [auth A], D [auth B]	4-{[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]sulfonyl}-2-(3-methylphenoxy)benzoic acid C24 H25 N3 O7 S HYOKWKXYBOKTDO-KRWDZBQOSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
T05	IC50 :  174   nM  PDBBind
T05	IC50:  174   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.199 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.2	α = 90
b = 90.97	β = 102.85
c = 48.33	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
AMoRE	phasing
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-16 
• Released Date: 2012-10-31 
Deposition Author(s): Boriack-Sjodin, A., Olivier, N.

Revision History  

• Version 1.0: 2012-10-31
  Type: Initial release
  
• Version 1.1: 2013-01-02
  Changes: Database references