4HWT

Crystal structure of human Threonyl-tRNA synthetase bound to a novel inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.207 

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:  4HWO, 4HWP, 4HWR, 4HWS

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Threonine--tRNA ligase, cytoplasmic
A, B
413Homo sapiensGene Names: TARS
EC: 6.1.1.3
Find proteins for P26639 (Homo sapiens)
Go to Gene View: TARS
Go to UniProtKB:  P26639
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1B2
Query on 1B2

Download SDF File 
Download CCD File 
A, 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 SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1B2Ki: >50000 nM BINDINGMOAD
1B2Ki: 50000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.207 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 73.897α = 90.00
b = 73.897β = 90.00
c = 357.587γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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