3T0T

Crystal structure of S. aureus Pyruvate Kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Cheminformatics-driven discovery of selective, nanomolar inhibitors for staphylococcal pyruvate kinase.

Axerio-Cilies, P.See, R.H.Zoraghi, R.Worral, L.Lian, T.Stoynov, N.Jiang, J.Kaur, S.Jackson, L.Gong, H.Swayze, R.Amandoron, E.Kumar, N.S.Moreau, A.Hsing, M.Strynadka, N.C.McMaster, W.R.Finlay, B.B.Foster, L.J.Young, R.N.Reiner, N.E.Cherkasov, A.

(2012) ACS Chem Biol 7: 350-359

  • DOI: 10.1021/cb2003576
  • Primary Citation of Related Structures:  
    3T0T

  • PubMed Abstract: 
  • We have recently mapped the protein interaction network of methicillin-resistant Staphylococcus aureus (MRSA), which revealed its scale-free organization with characteristic presence of highly connected hub proteins that are critical for bacterial survival ...

    We have recently mapped the protein interaction network of methicillin-resistant Staphylococcus aureus (MRSA), which revealed its scale-free organization with characteristic presence of highly connected hub proteins that are critical for bacterial survival. Here we report the discovery of inhibitors that are highly potent against one such hub target, staphylococcal pyruvate kinase (PK). Importantly, the developed compounds demonstrate complete selectivity for the bacterial enzyme compared to all human orthologues. The lead 91nM inhibitor IS-130 has been identified through ligand-based cheminformatic exploration of a chemical space around micromolar hits initially generated by experimental screening. The following crystallographic study resulted in identification of a tetrameric MRSA PK structure where IS-130 is bound to the interface between the protein's subunits. This newly described binding pocket is not present in otherwise highly similar human orthologues and can be effectively utilized for selective inhibition of bacterial PK. The following synthetic modifications of IS-130, guided by structure-based molecular modeling, resulted in the development of MRSA PK inhibitors with much improved antimicrobial properties. Considering a notable lack of recent reports on novel antibacterial targets and cognate antibacterial compounds, this study provides a valuable perspective on the development of a new generation of antimicrobials. Equally noteworthy, the results of the current work highlight the importance of rigorous cheminformatics-based exploration of the results of high-throughput experiments.


    Organizational Affiliation

    Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyruvate kinaseA, B, C, D606Staphylococcus aureus subsp. aureus MRSA252Mutation(s): 0 
Gene Names: pykSAR1776
EC: 2.7.1.40
UniProt
Find proteins for Q6GG09 (Staphylococcus aureus (strain MRSA252))
Explore Q6GG09 
Go to UniProtKB:  Q6GG09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6GG09
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I30
Query on I30

Download Ideal Coordinates CCD File 
E [auth A],
I [auth D]
N'-[(1E)-1-(1H-benzimidazol-2-yl)ethylidene]-5-bromo-2-hydroxybenzohydrazide
C16 H13 Br N4 O2
QYPYMNJXDLGLRD-AWQFTUOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A],
G [auth B],
H [auth C],
J [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
I30 PDBBind:  3T0T IC50: 91 (nM) from 1 assay(s)
BindingDB:  3T0T IC50: 91 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.09α = 90
b = 113.09β = 90
c = 315.96γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MxDCdata collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-06
    Type: Initial release