3V8P

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a new di-adenosine inhibitor formed in situ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Screening and In Situ Synthesis Using Crystals of a NAD Kinase Lead to a Potent Antistaphylococcal Compound.

Gelin, M.Poncet-Montange, G.Assairi, L.Morellato, L.Huteau, V.Dugue, L.Dussurget, O.Pochet, S.Labesse, G.

(2012) Structure 20: 1107-1117

  • DOI: https://doi.org/10.1016/j.str.2012.03.024
  • Primary Citation of Related Structures:  
    3V7U, 3V7W, 3V7Y, 3V80, 3V8M, 3V8N, 3V8P, 3V8Q, 3V8R

  • PubMed Abstract: 

    Making new ligands for a given protein by in situ ligation of building blocks (or fragments) is an attractive method. However, it suffers from inherent limitations, such as the limited number of available chemical reactions and the low information content of usual chemical library deconvolution. Here, we describe a focused screening of adenosine derivatives using X-ray crystallography. We discovered an unexpected and biocompatible chemical reactivity and have simultaneously identified the mode of binding of the resulting products. We observed that the NAD kinase from Listeria monocytogenes (LmNADK1) can promote amide formation between 5'-amino-5'-deoxyadenosine and carboxylic acid groups. This unexpected reactivity allowed us to bridge in situ two adenosine derivatives to fully occupy the active NAD site. This guided the design of a close analog showing micromolar inhibition of two human pathogenic NAD kinases and potent bactericidal activity against Staphylococcus aureus in vitro.


  • Organizational Affiliation

    Atelier de Bio- et Chimie Informatique Structurale, Centre de Biochimie Structurale, CNRS, UMR5048, Universités Montpellier 1 et 2, F-34090 Montpellier, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable inorganic polyphosphate/ATP-NAD kinase 1272Listeria monocytogenesMutation(s): 0 
Gene Names: ppnK1lmo0968
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZNB
Query on ZNB

Download Ideal Coordinates CCD File 
C [auth A]2-[6-azanyl-9-[(2R,3R,4S,5R)-5-[[(azanylidene-$l^{4}-azanylidene)amino]methyl]-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]sulfanyl-N-[[(2R,3S,4R,5R)-5-(6-azanyl-8-bromanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]ethanamide
C22 H25 Br N14 O7 S
WFFKQQMGOXMIGR-ZOUOOXKVSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
B [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.95α = 90
b = 75.64β = 90
c = 118.76γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2012-06-06
    Changes: Database references
  • Version 1.2: 2012-06-27
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2020-06-24
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-02-28
    Changes: Data collection, Database references, Derived calculations
  • Version 2.0: 2024-05-15
    Changes: Data collection, Non-polymer description, Structure summary