4HWT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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, 4HWT

  • 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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Threonine--tRNA ligase, cytoplasmicA, B413Homo sapiensMutation(s): 0 
Gene Names: TARSTARS1
EC: 6.1.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P26639 (Homo sapiens)
Explore P26639 
Go to UniProtKB:  P26639
PHAROS:  P26639
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26639
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
Binding Affinity Annotations 
IDSourceBinding Affinity
1B2 PDBBind:  4HWT Ki: 5.00e+4 (nM) from 1 assay(s)
Binding MOAD:  4HWT Ki: 5.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.897α = 90
b = 73.897β = 90
c = 357.587γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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