7BZJ

The Discovery of Benzhydrol-Oxaborole Hybrid Derivatives as Leucyl-tRNA Synthetase Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

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This is version 1.2 of the entry. See complete history


Literature

Discovery of benzhydrol-oxaborole derivatives as Streptococcus pneumoniae leucyl-tRNA synthetase inhibitors.

Hao, G.Li, H.Yang, F.Dong, D.Li, Z.Ding, Y.Pan, W.Wang, E.Liu, R.Zhou, H.

(2021) Bioorg Med Chem 29: 115871-115871

  • DOI: https://doi.org/10.1016/j.bmc.2020.115871
  • Primary Citation of Related Structures:  
    7BZJ

  • PubMed Abstract: 

    Pneumonia caused by bacterium S. pneumoniae is a severe acute respiratory infectious disease with high morbidity and mortality, especially for children and immunity-compromised patients. The emergence of multidrug-resistant S. pneumoniae also presents a challenge to human health. Leucyl-tRNA synthetase (LeuRS) catalyzes the attachment of l-leucine to tRNA Leu , which plays an essential role in protein translation and is considered an attractive antimicrobial drug target. In the present work, benzhydrol-oxaborole hybrid compounds were designed and synthesized as inhibitors of S. pneumoniae LeuRS. Exploration of the phenyl ring near Lysine 389 eventually yielded compounds 46 and 54 with submicromolar inhibitory potency. The co-crystal of compound 54 in the editing domain pocket of SpLeuRS was obtained and confirmed the formation of an additional hydrogen bond between the carbonyl of 54 and Lysine 389. It also showed anti-pneumococcal activity in vitro. The structure-activity relationship was discussed. This work will provide an essential foundation for the further development of anti-pneumococcal agents by targeting LeuRS.


  • Organizational Affiliation

    State Key Laboratory of Microbial Metabolism, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine--tRNA ligase192Streptococcus pneumoniae ATCC 700669Mutation(s): 1 
Gene Names: leuSSPN23F02440
EC: 6.1.1.4
UniProt
Find proteins for B8ZKS5 (Streptococcus pneumoniae (strain ATCC 700669 / Spain 23F-1))
Explore B8ZKS5 
Go to UniProtKB:  B8ZKS5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8ZKS5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FGX (Subject of Investigation/LOI)
Query on FGX

Download Ideal Coordinates CCD File 
B [auth A][(1~{R},5~{R},6~{S},8~{R})-8-(6-aminopurin-9-yl)-4'-[(~{R})-oxidanyl-[4-(2-oxidanylidenepropylsulfanyl)phenyl]methyl]spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,7'-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-triene]-6-yl]methoxy-tris(oxidanyl)phosphanium
C28 H31 B N5 O9 P S
YYNKFKBRIAWSCO-QTPLPVLTSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.373α = 90
b = 87.373β = 90
c = 135.528γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770842
National Natural Science Foundation of China (NSFC)China31971230

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description