4P74

PheRS in complex with compound 3a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The role of a novel auxiliary pocket in bacterial phenylalanyl-tRNA synthetase druggability.

Abibi, A.Ferguson, A.D.Fleming, P.R.Gao, N.Hajec, L.I.Hu, J.Laganas, V.A.McKinney, D.C.McLeod, S.M.Prince, D.B.Shapiro, A.B.Buurman, E.T.

(2014) J Biol Chem 289: 21651-21662

  • DOI: 10.1074/jbc.M114.574061
  • Primary Citation of Related Structures:  
    4P73, 4P74, 4P75, 4P71, 4P72

  • PubMed Abstract: 
  • The antimicrobial activity of phenyl-thiazolylurea-sulfonamides against Staphylococcus aureus PheRS are dependent upon phenylalanine levels in the extracellular fluids. Inhibitor efficacy in animal models of infection is substantially diminished by d ...

    The antimicrobial activity of phenyl-thiazolylurea-sulfonamides against Staphylococcus aureus PheRS are dependent upon phenylalanine levels in the extracellular fluids. Inhibitor efficacy in animal models of infection is substantially diminished by dietary phenylalanine intake, thereby reducing the perceived clinical utility of this inhibitor class. The search for novel antibacterial compounds against Gram-negative pathogens led to a re-evaluation of this phenomenon, which is shown here to be unique to S. aureus. Inhibition of macromolecular syntheses and characterization of novel resistance mutations in Escherichia coli demonstrate that antimicrobial activity of phenyl-thiazolylurea-sulfonamides is mediated by PheRS inhibition, validating this enzyme as a viable drug discovery target for Gram-negative pathogens. A search for novel inhibitors of PheRS yielded three novel chemical starting points. NMR studies were used to confirm direct target engagement for phenylalanine-competitive hits. The crystallographic structure of Pseudomonas aeruginosa PheRS defined the binding modes of these hits and revealed an auxiliary hydrophobic pocket that is positioned adjacent to the phenylalanine binding site. Three viable inhibitor-resistant mutants were mapped to this pocket, suggesting that this region is a potential liability for drug discovery.


    Organizational Affiliation

    From the Departments of Biosciences and Ed.Buurman@astrazeneca.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phenylalanine--tRNA ligase beta subunitA, B792Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: pheTPA2739
EC: 6.1.1.20
Find proteins for Q9I0A4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I0A4 
Go to UniProtKB:  Q9I0A4
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Phenylalanine--tRNA ligase alpha subunitC, D338Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: pheSPA2740
EC: 6.1.1.20
Find proteins for Q9I0A3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I0A3 
Go to UniProtKB:  Q9I0A3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2U9
Query on 2U9

Download CCD File 
C, D
N-[(3S)-1,1-dioxidotetrahydrothiophen-3-yl]-2-[(4-methylphenoxy)methyl]-1,3-thiazole-4-carboxamide
C16 H18 N2 O4 S2
VINDBUONEPJWMV-LBPRGKRZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2U9IC50:  80000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.06α = 90
b = 219.26β = 101.88
c = 107.4γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
Cootmodel building
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-03-25 
  • Released Date: 2014-06-25 
  • Deposition Author(s): Ferguson, A.D.

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy