6CHN

Phosphopantetheine adenylyltransferase (CoaD) in complex with methyl (R)-4-(3-(2-cyano-1-((5-methyl-7-oxo-4,7-dihydro-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)amino)ethyl)phenoxy)piperidine-1-carboxylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.163 

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 4 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
PG4
Query on PG4

Download SDF File 
Download CCD File 
A, B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
F1D
Query on F1D

Download SDF File 
Download CCD File 
A, B
methyl 4-(3-{(1R)-2-cyano-1-[(5-methyl-7-oxo-6,7-dihydro[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)amino]ethyl}phenoxy)piperidine-1-carboxylate
C22 H25 N7 O4
BAVCOKCQUYWPLU-GOSISDBHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F1DKd: 11 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.163 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 134.804α = 90.00
b = 134.804β = 90.00
c = 134.804γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
X-Areadata reduction
PHASERphasing
REFMACrefinement
Aimlessdata scaling

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