5T2Y

Crystal Structure of C. jejuni PglD in complex with 5-methyl-4-(methylamino)-2-phenethylthieno[2,3-d]pyrimidine-6-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Targeting Bacillosamine Biosynthesis in Bacterial Pathogens: Development of Inhibitors to a Bacterial Amino-Sugar Acetyltransferase from Campylobacter jejuni.

De Schutter, J.W.Morrison, J.P.Morrison, M.J.Ciulli, A.Imperiali, B.

(2017) J Med Chem 60: 2099-2118

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b01869
  • Primary Citation of Related Structures:  
    5T2Y, 5TYH

  • PubMed Abstract: 

    The glycoproteins of selected microbial pathogens often include highly modified carbohydrates such as 2,4-diacetamidobacillosamine (diNAcBac). These glycoconjugates are involved in host-cell interactions and may be associated with the virulence of medically significant Gram-negative bacteria. In light of genetic studies demonstrating the attenuated virulence of bacterial strains in which modified carbohydrate biosynthesis enzymes have been knocked out, we are developing small molecule inhibitors of selected enzymes as tools to evaluate whether such compounds modulate virulence. We performed fragment-based and high-throughput screens against an amino-sugar acetyltransferase enzyme, PglD, involved in biosynthesis of UDP-diNAcBac in Campylobacter jejuni. Herein we report optimization of the hits into potent small molecule inhibitors (IC 50 < 300 nM). Biophysical characterization shows that the best inhibitors are competitive with acetyl coenzyme A and an X-ray cocrystal structure reveals that binding is biased toward occupation of the adenine subpocket of the AcCoA binding site by an aromatic ring.


  • Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-acetylbacillosamine N-acetyltransferase
A, B
198Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819Mutation(s): 0 
Gene Names: pglDCj1123c
EC: 2.3.1.203
UniProt
Find proteins for Q0P9D1 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168))
Explore Q0P9D1 
Go to UniProtKB:  Q0P9D1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0P9D1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
753 Binding MOAD:  5T2Y IC50: 2200 (nM) from 1 assay(s)
BindingDB:  5T2Y IC50: 2200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.696α = 90
b = 106.696β = 90
c = 46.941γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM097241
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesR03 MH096549

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-22
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence