4UFZ | pdb_00004ufz

Synthesis of Novel NAD Dependant DNA Ligase Inhibitors via Negishi Cross-Coupling: Development of SAR and Resistance Studies


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 
    0.250 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted IA7Click on this verticalbar to view detailsBest fitted IWHClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Negishi Cross-Coupling Enabled Synthesis of Novel Nad(+)-Dependent DNA Ligase Inhibitors and Sar Development.

Murphy-Benenato, K.E.Gingipalli, L.Boriack-Sjodin, P.A.Martinez-Botella, G.Carcanague, D.Eyermann, C.J.Gowravaram, M.Harang, J.Hale, M.R.Ioannidis, G.Jahic, H.Johnstone, M.Kutschke, A.Laganas, V.A.Loch, J.T.Miller, M.D.Oguto, H.Patel, S.J.

(2015) Bioorg Med Chem Lett 25: 5172

  • DOI: https://doi.org/10.1016/j.bmcl.2015.09.075
  • Primary Citation of Related Structures:  
    4UFZ

  • PubMed Abstract: 

    Two novel compounds, pyridopyrimidines (1) and naphthyridines (2) were identified as potent inhibitors of bacterial NAD(+)-dependent DNA ligase (Lig) A in a fragment screening. SAR was guided by molecular modeling and X-ray crystallography. It was observed that the diaminonitrile pharmacophore made a key interaction with the ligase enzyme, specifically residues Glu114, Lys291, and Leu117. Synthetic challenges limited opportunities for diversification of the naphthyridine core, therefore most of the SAR was focused on a pyridopyrimidine scaffold. The initial diversification at R(1) improved both enzyme and cell potency. Further SAR developed at the R(2) position using the Negishi cross-coupling reaction provided several compounds, among these compounds 22g showed good enzyme potency and cellular potency.


  • Organizational Affiliation

    Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA LIGASE324Haemophilus influenzaeMutation(s): 0 
EC: 6.5.1.2
UniProt
Find proteins for P43813 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P43813 
Go to UniProtKB:  P43813
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43813
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IA7
Query on IA7

Download Ideal Coordinates CCD File 
B [auth A]5,7-bis(azanyl)-2-tert-butyl-4-(1,3-thiazol-2-yl)pyrido[2,3-d]pyrimidine-6-carbonitrile
C15 H15 N7 S
VDKRFQKJPXSMOG-UHFFFAOYSA-N
IWH
Query on IWH

Download Ideal Coordinates CCD File 
C [auth A]1-(2,4-dimethylbenzyl)-6-oxo-1,6-dihydropyridine-3-carboxamide
C15 H16 N2 O2
TUJVPUNUHQIBSM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free:  0.250 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.814α = 90
b = 138.814β = 90
c = 56.165γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
d*TREKdata reduction
DTSCALEdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted IA7Click on this verticalbar to view detailsBest fitted IWHClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2015-11-11
    Changes: Database references
  • Version 1.2: 2018-04-04
    Changes: Data collection
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other