6CHP

Phosphopantetheine adenylyltransferase (CoaD) in complex with methyl (R)-4-(3-(2-cyano-1-((5-methyl-1H-imidazo[4,5-b]pyridin-2-yl)amino)ethyl)benzyl)piperidine-1-carboxylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acs.jmedchem.7b01861
  • Primary Citation of Related Structures:  
    6CHL, 6CHM, 6CHN, 6CHO, 6CHP, 6CHQ, 6CKW

  • 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). 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphopantetheine adenylyltransferase
A, B
161Escherichia coli K-12Mutation(s): 0 
Gene Names: coaDkdtByicAb3634JW3609
EC: 2.7.7.3
UniProt
Find proteins for P0A6I6 (Escherichia coli (strain K12))
Explore P0A6I6 
Go to UniProtKB:  P0A6I6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6I6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F0Y
Query on F0Y

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
methyl 4-[(3-{(1R)-2-cyano-1-[(5-methyl-3H-imidazo[4,5-b]pyridin-2-yl)amino]ethyl}phenyl)methyl]piperidine-1-carboxylate
C24 H28 N6 O2
NAKOGAFXAQIHDB-HXUWFJFHSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
L [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
I [auth B],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.634α = 90
b = 135.634β = 90
c = 135.634γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
X-Areadata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2018-05-09
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references