4HWO

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

• PDB DOI: https://doi.org/10.2210/pdb4HWO/pdb

• Classification: Ligase/Ligase Inhibitor
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.200 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 

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.

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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: 96.93 kDa 
• Atom Count: 7,208 
• Modelled Residue Count: 807 
• Deposited Residue Count: 822 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Threonine--tRNA ligase	A, B	411	Escherichia coli K-12	Mutation(s): 0  Gene Names: thrS, b1719, JW1709 EC: 6.1.1.3
UniProt
Find proteins for P0A8M3 (Escherichia coli (strain K12)) Explore P0A8M3  Go to UniProtKB:  P0A8M3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
409	D [auth A], F [auth B]	N-{[3-(4-aminoquinazolin-7-yl)phenyl]sulfonyl}-L-threoninamide C18 H19 N5 O4 S QIPHQMPGDDKWIL-HWPZZCPQSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
409	PDBBind:  4HWO	Ki: 2.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.200 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.9	α = 90
b = 110.3	β = 90
c = 114.36	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

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
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Refinement description