8OU8

Crystal structure of E. coli threonyl tRNA synthetase in complex with a TM84 analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.216 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Synthesis and evaluation of an agrocin 84 toxic moiety (TM84) analogue as a malarial threonyl tRNA synthetase inhibitor.

Buitrago, J.A.R.Leitis, G.Kanepe-Lapsa, I.Rudnickiha, A.Parisini, E.Jirgensons, A.

(2023) Org Biomol Chem 21: 5433-5439

  • DOI: https://doi.org/10.1039/d3ob00670k
  • Primary Citation of Related Structures:  
    8OU8

  • PubMed Abstract: 

    An analogue of a toxic moiety (TM84) of natural product agrocin 84 containing threonine amide instead of 2,3-dihydroxy-4-methylpentanamide was prepared and evaluated as a putative Plasmodium falciparum threonyl t-RNA synthetase (PfThrRS) inhibitor. This TM84 analogue features submicromolar inhibitory potency (IC 50 = 440 nM) comparable to that of borrelidin (IC 50 = 43 nM) and therefore complements chemotypes known to inhibit malarial PfThrRS, which are currently limited to borrelidin and its analogues. The crystal structure of the inhibitor in complex with the E. coli homologue enzyme (EcThrRS) was obtained, revealing crucial ligand-protein interactions that will pave the way for the design of novel ThrRS inhibitors.


  • Organizational Affiliation

    Latvian Institute of Organic Synthesis, Riga LV-1006, Latvia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Threonine--tRNA ligaseA [auth D],
B [auth A]
411Escherichia coli IAI1Mutation(s): 0 
Gene Names: thrSECIAI1_1775
EC: 6.1.1.3
UniProt
Find proteins for P0A8M3 (Escherichia coli (strain K12))
Explore P0A8M3 
Go to UniProtKB:  P0A8M3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8M3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
W0U
Query on W0U

Download Ideal Coordinates CCD File 
C [auth D],
G [auth A]
[(2~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methoxy-~{N}-[(2~{S},3~{S})-2-azanyl-3-oxidanyl-butanoyl]phosphonamidic acid
C14 H22 N7 O7 P
ATWLNPAQYPTPKC-UDFANUMJSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
D,
H [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth D],
J [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
I [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.33α = 90
b = 108.95β = 90
c = 113.96γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
xia2.multiplexdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Regional Development FundEuropean Union1.1.1.1/19/A/019

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-07-19
    Changes: Database references
  • Version 1.2: 2023-09-06
    Changes: Data collection