5DHQ

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a novel inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

8-Thioalkyl-adenosine derivatives inhibit Listeria monocytogenes NAD kinase through a novel binding mode.

Paoletti, J.Assairi, L.Gelin, M.Huteau, V.Nahori, M.A.Dussurget, O.Labesse, G.Pochet, S.

(2016) Eur.J.Med.Chem. 124: 1041-1056

  • DOI: 10.1016/j.ejmech.2016.10.033
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Increased resistance of pathogens to existing antibiotics necessitates the search for novel targets to develop potent antimicrobials. Biosynthetic pathways of several cofactors important for bacterial growth, such as nicotinamide adenine dinucleotide ...

    Increased resistance of pathogens to existing antibiotics necessitates the search for novel targets to develop potent antimicrobials. Biosynthetic pathways of several cofactors important for bacterial growth, such as nicotinamide adenine dinucleotide phosphate (NADP), have been proposed as a promising source of antibiotic targets. Nicotinamide adenine dinucleotide kinases (NADK; EC 2.7.1.23) are attractive for inhibitor development, since they catalyze the phosphorylation of NAD to NADP, which is an essential step of NADP metabolism. We previously synthesized diadenosine derivatives that inhibited NADK from two human pathogens, Listeria monocytogenes and Staphylococcus aureus, in the micromolar range. They behave as NAD mimics with the 5',5'-diphosphate group substituted by a 8,5' thioglycolic bridge. In an attempt to improve inhibitory potency, we designed new NAD mimics based on a single adenosine moiety harboring a larger derivatization attached to the C8 position and a small group at the 5' position. Here we report the synthesis of a series of 8-thioalkyl-adenosine derivatives containing various aryl and heteroaryl moieties and their evaluation as inhibitors of L. monocytogenes NADK1, S. aureus NADK and their human counterpart. Novel, sub-micromolar inhibitors of LmNADK1 were identified. Surprisingly, most LmNADK1 inhibitors demonstrated a high selectivity index against the close staphylococcal ortholog and the human NADK. Structural characterization of enzyme-inhibitor complexes revealed the original binding mode of these novel NAD mimics.


    Organizational Affiliation

    CNRS, UMR5048, Université Montpellier, Centre de Biochimie Structurale, 29, route de Navacelles, 34090, Montpellier, France; INSERM, U1054, Montpellier, France.,Institut Pasteur, Unité de Chimie et Biocatalyse, 28 rue du Dr Roux, 75724, Paris cedex 15, France; CNRS, UMR3523, Paris, France.,Institut Pasteur, Unité des Interactions Bactéries-Cellules, 25 rue du Dr Roux, 75724 Paris cedex 15, France; INSERM, U604, Paris, France; INRA, USC2020, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Institut Pasteur, Unité de Chimie et Biocatalyse, 28 rue du Dr Roux, 75724, Paris cedex 15, France; CNRS, UMR3523, Paris, France. Electronic address: sylvie.pochet@pasteur.fr.,INSERM, U759, Institut Curie, 91405, Orsay, France.,Institut Pasteur, Unité des Interactions Bactéries-Cellules, 25 rue du Dr Roux, 75724 Paris cedex 15, France; INSERM, U604, Paris, France; INRA, USC2020, Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD kinase 1
A, B, C, D
272Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)Mutation(s): 0 
Gene Names: nadK1
EC: 2.7.1.23
Find proteins for Q8Y8D7 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Go to UniProtKB:  Q8Y8D7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A, B
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
5AK
Query on 5AK

Download SDF File 
Download CCD File 
A, B, C, D
8-[(2-{[2-(3-bromophenyl)ethyl]amino}-2-oxoethyl)sulfanyl]adenosine
C20 H23 Br N6 O5 S
WJGLUXUMEHFNOZ-BGIGGGFGSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5AKKi: 2000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.260 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.790α = 90.00
b = 119.180β = 99.91
c = 67.210γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-10-INSB-05-01

Revision History 

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-11-09
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Data collection