6RC0

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complexe with an adenine derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

From Substrate to Fragments to Inhibitor ActiveIn VivoagainstStaphylococcus aureus.

Gelin, M.Paoletti, J.Nahori, M.A.Huteau, V.Leseigneur, C.Jouvion, G.Dugue, L.Clement, D.Pons, J.L.Assairi, L.Pochet, S.Labesse, G.Dussurget, O.

(2020) ACS Infect Dis 6: 422-435

  • DOI: https://doi.org/10.1021/acsinfecdis.9b00368

  • PubMed Abstract: 

    Antibiotic resistance is a worldwide threat due to the decreasing supply of new antimicrobials. Novel targets and innovative strategies are urgently needed to generate pathbreaking drug compounds. NAD kinase (NADK) is essential for growth in most bacteria, as it supports critical metabolic pathways. Here, we report the discovery of a new class of antibacterials that targets bacterial NADK. We generated a series of small synthetic adenine derivatives to screen those harboring promising substituents in order to guide efficient fragment linking. This led to NKI1, a new lead compound inhibiting NADK that showed in vitro bactericidal activity against Staphylococcus aureus . In a murine model of infection, NKI1 restricted survival of the bacteria, including methicillin-resistant S. aureus . Collectively, these findings identify bacterial NADK as a potential drug target and NKI1 as a lead compound in the treatment of staphylococcal infections.


  • Organizational Affiliation

    Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université Montpellier, 29 route de Navacelles, 34090 Montpellier, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD kinase 1272Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: nadK1lmo0968
EC: 2.7.1.23
UniProt
Find proteins for Q8Y8D7 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore Q8Y8D7 
Go to UniProtKB:  Q8Y8D7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8Y8D7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.11α = 90
b = 78.19β = 90
c = 117.96γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
ADSCdata collection
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-03-25
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references, Refinement description