6CHQ

Phosphopantetheine adenylyltransferase (CoaD) in complex with 2-benzyl-N-(3-chloro-4-methylphenyl)-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphopantetheine adenylyltransferaseA, B161Escherichia 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F0V
Query on F0V

Download Ideal Coordinates CCD File 
C [auth A]2-benzyl-7-[(3-chloro-4-methylphenyl)amino]-5-methyl-3H-[1,2,4]triazolo[1,5-a]pyrimidin-8-ium
C20 H19 Cl N5
QGHMESXINCFELP-UHFFFAOYSA-O
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
G [auth A],
H [auth B],
I [auth B],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
F0V Binding MOAD:  6CHQ IC50: 4400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.189α = 90
b = 134.189β = 90
c = 134.189γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata 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