Staphylococcus aureus Type II pantothenate kinase in complex with a pantothenate analog

Experimental Data Snapshot

  • Resolution: 1.42 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

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This is version 1.3 of the entry. See complete history


Discovery of Potent Pantothenamide Inhibitors of Staphylococcus aureus Pantothenate Kinase through a Minimal SAR Study: Inhibition Is Due to Trapping of the Product.

Hughes, S.J.Barnard, L.Mottaghi, K.Tempel, W.Antoshchenko, T.Hong, B.S.Allali-Hassani, A.Smil, D.Vedadi, M.Strauss, E.Park, H.W.

(2016) ACS Infect Dis 2: 627-641

  • DOI: https://doi.org/10.1021/acsinfecdis.6b00090
  • Primary Citation of Related Structures:  
    4M7X, 4M7Y, 5ELZ, 5JIC

  • PubMed Abstract: 

    The potent antistaphylococcal activity of N-substituted pantothenamides (PanAms) has been shown to at least partially be due to the inhibition of Staphylococcus aureus's atypical type II pantothenate kinase (SaPanK II ), the first enzyme of coenzyme A biosynthesis. This mechanism of action follows from SaPanK II having a binding mode for PanAms that is distinct from those of other PanKs. To dissect the molecular interactions responsible for PanAm inhibitory activity, we conducted a mini SAR study in tandem with the cocrystallization of SaPanK II with two classic PanAms (N5-Pan and N7-Pan), culminating in the synthesis and characterization of two new PanAms, N-Pip-PanAm and MeO-N5-PanAm. The cocrystal structures showed that all of the PanAms are phosphorylated by SaPanK II but remain bound at the active site; this occurs primarily through interactions with Tyr240' and Thr172'. Kinetic analysis showed a strong correlation between k cat (slow PanAm turnover) and IC 50 (inhibition of pantothenate phosphorylation) values, suggesting that SaPanK II inhibition occurs via a delay in product release. In-depth analysis of the PanAm-bound structures showed that the capacity for accepting a hydrogen bond from the amide of Thr172' was a stronger determinant for PanAm potency than the capacity to π-stack with Tyr240'. The two new PanAms, N-Pip-PanAm and MeO-N5-PanAm, effectively combine both hydrogen bonding and hydrophobic interactions, resulting in the most potent SaPanK II inhibition described to date. Taken together, our results are consistent with an inhibition mechanism wherein PanAms act as SaPanK II substrates that remain bound upon phosphorylation. The phospho-PanAm-SaPanK II interactions described herein may help future antistaphylococcal drug development.

  • Organizational Affiliation

    Department of Biochemistry, Stellenbosch University , Stellenbosch 7600, South Africa.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Type II pantothenate kinase273Staphylococcus aureus subsp. aureus MW2Mutation(s): 0 
Gene Names: coaWMW2054
Find proteins for Q8NVG0 (Staphylococcus aureus (strain MW2))
Explore Q8NVG0 
Go to UniProtKB:  Q8NVG0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NVG0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
C10 H15 N5 O10 P2
Query on 27Q

Download Ideal Coordinates CCD File 
P [auth A]N-heptyl-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide
C16 H33 N2 O7 P
Query on MG

Download Ideal Coordinates CCD File 
Query on UNX

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.42 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.92α = 90
b = 136.53β = 90
c = 73.62γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2016-12-28
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description