4HWT

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

• PDB DOI: https://doi.org/10.2210/pdb4HWT/pdb

• Classification: Ligase/Ligase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


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

---

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 

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

• PubMed: 23362938 
• DOI: https://doi.org/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. 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. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 97.83 kDa 
• Atom Count: 6,972 
• Modelled Residue Count: 797 
• Deposited Residue Count: 826 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Threonine--tRNA ligase, cytoplasmic	A, B	413	Homo sapiens	Mutation(s): 0  Gene Names: TARS 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 GTEx:  ENSG00000113407

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1B2	D [auth A], F [auth B]	N-{[3-(2H-indazol-5-yl)phenyl]sulfonyl}-L-threoninamide C17 H18 N4 O4 S RDKBQXPBHLCILS-HWPZZCPQSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1B2	Binding MOAD:  4HWT	Ki: 5.00e+4 (nM) from 1 assay(s)
	PDBBind:  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 = 73.897	α = 90
b = 73.897	β = 90
c = 357.587	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data reduction
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

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