4P73

PheRS in complex with compound 1a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1074/jbc.M114.574061
  • Primary Citation of Related Structures:  
    4P71, 4P72, 4P73, 4P74, 4P75

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phenylalanine--tRNA ligase beta subunit
A, B
792Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: pheTPA2739
EC: 6.1.1.20
UniProt
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I0A4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phenylalanine--tRNA ligase alpha subunit
C, D
338Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: pheSPA2740
EC: 6.1.1.20
UniProt
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I0A3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GAX
Query on GAX

Download Ideal Coordinates CCD File 
E [auth C],
F [auth D]
1-{3-[(4-pyridin-2-ylpiperazin-1-yl)sulfonyl]phenyl}-3-(1,3-thiazol-2-yl)urea
C19 H20 N6 O3 S2
NJPVZSIGDRLLTD-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
GAX BindingDB:  4P73 IC50: 22 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.29α = 90
b = 220.05β = 101.76
c = 107.93γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
Aimlessdata scaling
Cootmodel building
ROVERSIrefinement
SHARFFrefinement
SMARTrefinement
VONRHEINrefinement
MATTHEWSrefinement
TRONRUDrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description