3V7Y

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 5'-N-Propargylamino-5'-deoxyadenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1016/j.str.2012.03.024
  • Primary Citation of Related Structures:  
    3V80, 3V8M, 3V8N, 3V8P, 3V8Q, 3V8R, 3V7U, 3V7W, 3V7Y

  • 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 co ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable inorganic polyphosphate/ATP-NAD kinase 1A272Listeria monocytogenesMutation(s): 0 
Gene Names: ppnK1lmo0968
EC: 2.7.1.23
Find proteins for Q8Y8D7 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore Q8Y8D7 
Go to UniProtKB:  Q8Y8D7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A3N
Query on A3N

Download CCD File 
A
5'-deoxy-5'-(prop-2-yn-1-ylamino)adenosine
C13 H16 N6 O3
WYZJLWUBEMXBJJ-QYVSTXNMSA-N
 Ligand Interaction
CIT
Query on CIT

Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.812α = 90
b = 75.675β = 90
c = 118.619γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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