7AP4

Thermus thermophilus Aspartyl-tRNA Synthetase in Complex with Compound AspS7HMDDA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Synthesis and Biological Evaluation of 1,3-Dideazapurine-Like 7-Amino-5-Hydroxymethyl-Benzimidazole Ribonucleoside Analogues as Aminoacyl-tRNA Synthetase Inhibitors.

Zhang, B.Pang, L.Nautiyal, M.De Graef, S.Gadakh, B.Lescrinier, E.Rozenski, J.Strelkov, S.V.Weeks, S.D.Van Aerschot, A.

(2020) Molecules 25

  • DOI: https://doi.org/10.3390/molecules25204751
  • Primary Citation of Related Structures:  
    7AP1, 7AP2, 7AP3, 7AP4

  • PubMed Abstract: 

    Aminoacyl-tRNA synthetases (aaRSs) have become viable targets for the development of antimicrobial agents due to their crucial role in protein translation. A series of six amino acids were coupled to the purine-like 7-amino-5-hydroxymethylbenzimidazole nucleoside analogue following an optimized synthetic pathway. These compounds were designed as aaRS inhibitors and can be considered as 1,3-dideazaadenine analogues carrying a 2-hydroxymethyl substituent. Despite our intentions to obtain N 1 -glycosylated 4-aminobenzimidazole congeners, resembling the natural purine nucleosides glycosylated at the N 9 -position, we obtained the N 3 -glycosylated benzimidazole derivatives as the major products, resembling the respective purine N 7 -glycosylated nucleosides. A series of X-ray crystal structures of class I and II aaRSs in complex with newly synthesized compounds revealed interesting interactions of these "base-flipped" analogues with their targets. While the exocyclic amine of the flipped base mimics the reciprocal interaction of the N 3 -purine atom of aminoacyl-sulfamoyl adenosine (aaSA) congeners, the hydroxymethyl substituent of the flipped base apparently loses part of the standard interactions of the adenine N 1 and the N 6 -amine as seen with aaSA analogues. Upon the evaluation of the inhibitory potency of the newly obtained analogues, nanomolar inhibitory activities were noted for the leucine and isoleucine analogues targeting class I aaRS enzymes, while rather weak inhibitory activity against the corresponding class II aaRSs was observed. This class bias could be further explained by detailed structural analysis.


  • Organizational Affiliation

    Rega Institute for Medical Research, Medicinal Chemistry, KU Leuven, Herestraat 49-box 1041, 3000 Leuven, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate--tRNA(Asp) ligase
A, B
581Thermus thermophilus HB8Mutation(s): 0 
Gene Names: aspS1TTHA0711
EC: 6.1.1.12
UniProt
Find proteins for Q5SKD2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SKD2 
Go to UniProtKB:  Q5SKD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SKD2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RSN (Subject of Investigation/LOI)
Query on RSN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(3~{S})-3-azanyl-4-[[(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxysulfonylamino]-4-oxidanylidene-butanoic acid
C17 H23 N5 O10 S
NPTGVUDUYJMSLG-OULBZCFASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.277α = 90
b = 112.531β = 104.86
c = 88.253γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)Belgium1S53518N

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description