6CHM

Phosphopantetheine adenylyltransferase (CoaD) in complex with N-(2-(5-methoxy-1H-indol-3-yl)ethyl)pivalamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery and Optimization of Phosphopantetheine Adenylyltransferase Inhibitors with Gram-Negative Antibacterial Activity.

Skepper, C.K.Moreau, R.J.Appleton, B.A.Benton, B.M.Drumm, J.E.Feng, B.Y.Geng, M.Hu, C.Li, C.Lingel, A.Lu, Y.Mamo, M.Mergo, W.Mostafavi, M.Rath, C.M.Steffek, M.Takeoka, K.T.Uehara, K.Wang, L.Wei, J.R.Xie, L.Xu, W.Zhang, Q.de Vicente, J.

(2018) J. Med. Chem. 61: 3325-3349

  • DOI: 10.1021/acs.jmedchem.7b01861
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In the preceding manuscript [ Moreau et al. 2018 , 10.1021/acs.jmedchem.7b01691 ] we described a successful fragment-based lead discovery (FBLD) strategy for discovery of bacterial phosphopantetheine adenylyltransferase inhibitors (PPAT, CoaD). Follo ...

    In the preceding manuscript [ Moreau et al. 2018 , 10.1021/acs.jmedchem.7b01691 ] we described a successful fragment-based lead discovery (FBLD) strategy for discovery of bacterial phosphopantetheine adenylyltransferase inhibitors (PPAT, CoaD). Following several rounds of optimization two promising lead compounds were identified: triazolopyrimidinone 3 and 4-azabenzimidazole 4. Here we disclose our efforts to further optimize these two leads for on-target potency and Gram-negative cellular activity. Enabled by a robust X-ray crystallography system, our structure-based inhibitor design approach delivered compounds with biochemical potencies 4-5 orders of magnitude greater than their respective fragment starting points. Additional optimization was guided by observations on bacterial permeability and physicochemical properties, which ultimately led to the identification of PPAT inhibitors with cellular activity against wild-type E. coli.


    Organizational Affiliation

    Novartis Institutes for Biomedical Research, 5300 Chiron Way , Emeryville , California 94608 , United States.




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
F1V
Query on F1V

Download SDF File 
Download CCD File 
A, B
N-[2-(5-methoxy-1H-indol-3-yl)ethyl]-2,2-dimethylpropanamide
C16 H22 N2 O2
CUMVZJLZCUYFCZ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F1VIC50: 199000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.198 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 135.386α = 90.00
b = 135.386β = 90.00
c = 135.386γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling
X-Areadata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2018-05-09
    Type: Data collection, Database references