9VCE | pdb_00009vce

Crystal structure of Escherichia coli tryptophanyl-tRNA synthetase in complex with 71g


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 
    0.210 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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Literature

Structure-based design of tirabrutinib derivatives as inhibitors of bacterial tryptophanyl-tRNA synthetase.

Xia, K.Peng, X.Xiao, L.Huang, Q.Xu, J.Chen, B.Zhou, H.

(2025) Bioorg Chem 165: 108978-108978

  • DOI: https://doi.org/10.1016/j.bioorg.2025.108978
  • Primary Citation of Related Structures:  
    9VCE, 9VCI

  • PubMed Abstract: 

    The escalating threat of antibiotic resistance poses a critical challenge to global public health, necessitating the urgent development of novel therapeutic agents with distinct mechanisms of action and unique structural scaffolds. Tryptophanyl-tRNA synthetase (TrpRS) has emerged as a promising antibacterial target. Our previous study demonstrated that the clinically utilized Bruton's tyrosine kinase (BTK) inhibitor tirabrutinib, along with several of its analogues, can simultaneously occupy both the substrates l-Trp and tRNA Trp A76 binding sites of Escherichia coli tryptophanyl-tRNA synthetase (EcTrpRS), thereby effectively inhibiting its catalytic activity. Building on this finding, we employed structure-based drug design to systematically optimize the interactions of tirabrutinib analogues with the l-Trp and tRNA Trp binding sites, as well as to further extend the structure to the adjacent ATP binding site within the catalytic pocket of EcTrpRS to establish additional interactions, leading to the design and synthesis of 22 new derivatives. Among these, WRS22 (a racemic mixture) demonstrated the best binding to EcTrpRS, with a ΔT m value of 33.2 °C and 90 % inhibition rate at 10 μM concentration. Its binding affinity for EcTrpRS (K d  = 0.33 ± 0.03 μM) is superior to that of the positive control, indolmycin (K d  = 0.71 ± 0.1 μM). Notably, WRS22 displayed no affinity to human cytoplasmic TrpRS (HcTrpRS) and its interaction with human BTK is likely to be disrupted, indicating high degree of target selectivity. Therefore, the structure-guided design successfully developed new tirabrutinib analogues as inhibitors of bacterial TrpRS, presenting a promising lead compound for the development of AARS-based antibacterial agents.


  • Organizational Affiliation
    • State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophan--tRNA ligase
A, B
340Escherichia coliMutation(s): 0 
Gene Names: 
EC: 6.1.1.2
UniProt
Find proteins for E2QFN4 (Escherichia coli)
Explore E2QFN4 
Go to UniProtKB:  E2QFN4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE2QFN4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TYM
Query on TYM

Download Ideal Coordinates CCD File 
G [auth B]TRYPTOPHANYL-5'AMP
C21 H24 N7 O8 P
IFQVDHDRFCKAAW-SQIXAUHQSA-N
A1ERS (Subject of Investigation/LOI)
Query on A1ERS

Download Ideal Coordinates CCD File 
C [auth A]~{N}-[[3-[4-(6-azanyl-8-oxidanylidene-9-piperidin-4-yl-purin-7-yl)phenoxy]phenyl]methyl]ethanamide
C25 H27 N7 O3
RAUAFLDCBPAPHJ-UHFFFAOYSA-N
CLW
Query on CLW

Download Ideal Coordinates CCD File 
H [auth B]CHLORZOXAZONE
C7 H4 Cl N O2
TZFWDZFKRBELIQ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
I [auth B],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free:  0.210 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.176α = 90
b = 79.272β = 105.71
c = 77.616γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
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)China22177140

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release