6CCN

Crystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with (R)-2,4-dihydroxy-N-(2-(4-hydroxy-1H-benzo[d]imidazol-2-yl)ethyl)-3,3-dimethylbutanamide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

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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:  
    6CCK, 6CCL, 6CCM, 6CCN, 6CCO, 6CCQ, 6CCS

  • PubMed Abstract: 

    • The discovery and development of new antibiotics capable of curing infections due to multidrug-resistant and pandrug-resistant Gram-negative bacteria are 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 ...

    The discovery and development of new antibiotics capable of curing infections due to multidrug-resistant and pandrug-resistant Gram-negative bacteria are 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 Δ tolC mutant strain.

    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: coaD, kdtB, yicA, b3634, JW3609
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EXS
Query on EXS
Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]		(2R)-2,4-dihydroxy-N-[2-(7-hydroxy-1H-benzimidazol-2-yl)ethyl]-3,3-dimethylbutanamide
C15 H21 N3 O4
SKIDJNQZVCDYIE-ZDUSSCGKSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EXS Binding MOAD:  6CCN IC50: 3.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.06α = 90
b = 135.06β = 90
c = 135.06γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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