4HWR

Crystal structure of E. coli Threonyl-tRNA synthetase bound to a novel inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.267 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Identification of bacteria-selective threonyl-tRNA synthetase substrate inhibitors by structure-based design.

Teng, M.Hilgers, M.T.Cunningham, M.L.Borchardt, A.Locke, J.B.Abraham, S.Haley, G.Kwan, B.P.Hall, C.Hough, G.W.Shaw, K.J.Finn, J.

(2013) J Med Chem 56: 1748-1760

  • DOI: 10.1021/jm301756m
  • Primary Citation of Related Structures:  
    4HWS, 4HWT, 4HWO, 4HWP, 4HWR

  • PubMed Abstract: 
  • A series of potent and bacteria-selective threonyl-tRNA synthetase (ThrRS) inhibitors have been identified using structure-based drug design. These compounds occupied the substrate binding site of ThrRS and showed excellent binding affinities for all of the bacterial orthologues tested ...

    A series of potent and bacteria-selective threonyl-tRNA synthetase (ThrRS) inhibitors have been identified using structure-based drug design. These compounds occupied the substrate binding site of ThrRS and showed excellent binding affinities for all of the bacterial orthologues tested. Some of the compounds displayed greatly improved bacterial selectivity. Key residues responsible for potency and bacteria/human ThrRS selectivity have been identified. Antimicrobial activity has been achieved against wild-type Haemophilus influenzae and efflux-deficient mutants of Escherichia coli and Burkholderia thailandensis.


    Organizational Affiliation

    Medicinal Chemistry, Trius Therapeutics, Inc., 6310 Nancy Ridge Drive, San Diego, California 92121, United States. mteng@triusrx.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Threonine--tRNA ligaseA, B411Escherichia coli K-12Mutation(s): 0 
Gene Names: thrSb1719JW1709
EC: 6.1.1.3
UniProt
Find proteins for P0A8M3 (Escherichia coli (strain K12))
Explore P0A8M3 
Go to UniProtKB:  P0A8M3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1B2
Query on 1B2

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]N-{[3-(2H-indazol-5-yl)phenyl]sulfonyl}-L-threoninamide
C17 H18 N4 O4 S
RDKBQXPBHLCILS-HWPZZCPQSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1B2Ki :  182   nM  PDBBind
1B2Ki:  182   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.267 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.899α = 90
b = 109.777β = 123.76
c = 86.995γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-11-08 
  • Released Date: 2013-09-18 
  • Deposition Author(s): Hilgers, M.T.

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-18
    Type: Initial release