6CCM

Crystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with 2-((3-bromobenzyl)amino)-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7(4H)-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fragment-Based Drug Discovery of Inhibitors of Phosphopantetheine Adenylyltransferase from Gram-Negative Bacteria.

Moreau, R.J.Skepper, C.K.Appleton, B.A.Blechschmidt, A.Balibar, C.J.Benton, B.M.Drumm, J.E.Feng, B.Y.Geng, M.Li, C.Lindvall, M.K.Lingel, A.Lu, Y.Mamo, M.Mergo, W.Polyakov, V.Smith, T.M.Takeoka, K.Uehara, K.Wang, L.Wei, J.R.Weiss, A.H.Xie, L.Xu, W.Zhang, Q.de Vicente, J.

(2018) J. Med. Chem. 61: 3309-3324

  • DOI: 10.1021/acs.jmedchem.7b01691
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The discovery and development of new antibiotics capable of curing infections due to multidrug-resistant and pandrug-resistant Gram-negative bacteria is a major challenge with fundamental importance to our global healthcare system. Part of our broad ...

    The discovery and development of new antibiotics capable of curing infections due to multidrug-resistant and pandrug-resistant Gram-negative bacteria is a major challenge with fundamental importance to our global healthcare system. Part of our broad program at Novartis to address this urgent, unmet need includes the search for new agents that inhibit novel bacterial targets. Here we report the discovery and hit-to-lead optimization of new inhibitors of phosphopantetheine adenylyltransferase (PPAT) from Gram-negative bacteria. Utilizing a fragment-based screening approach, we discovered a number of unique scaffolds capable of interacting with the pantetheine site of E. coli PPAT and inhibiting enzymatic activity, including triazolopyrimidinone 6. Structure-based optimization resulted in the identification of two lead compounds as selective, small molecule inhibitors of bacterial PPAT: triazolopyrimidinone 53 and azabenzimidazole 54 efficiently inhibited E. coli and P. aeruginosa PPAT and displayed modest cellular potency against the efflux-deficient E. coli ΔtolC mutant strain.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphopantetheine adenylyltransferase
A, B
161Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: coaD (kdtB, yicA)
EC: 2.7.7.3
Find proteins for P0A6I6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6I6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EXP
Query on EXP

Download SDF File 
Download CCD File 
A
2-{[(3-bromophenyl)methyl]amino}-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7(6H)-one
C13 H12 Br N5 O
NONMKRIVUVFGSW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.169 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 135.533α = 90.00
b = 135.533β = 90.00
c = 135.533γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
BUSTERrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-05-09
    Type: Data collection, Database references