Crystal structure of TrmD from Pseudomonas aeruginosa in complex with active-site inhibitor

Experimental Data Snapshot

  • Resolution: 2.75 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Targeting the Bacterial Epitranscriptome for Antibiotic Development: Discovery of Novel tRNA-(N1G37) Methyltransferase (TrmD) Inhibitors.

Zhong, W.Koay, A.Ngo, A.Li, Y.Nah, Q.Wong, Y.H.Chionh, Y.H.Ng, H.Q.Koh-Stenta, X.Poulsen, A.Foo, K.McBee, M.Choong, M.L.El Sahili, A.Kang, C.Matter, A.Lescar, J.Hill, J.Dedon, P.

(2019) ACS Infect Dis 5: 326-335

  • DOI: https://doi.org/10.1021/acsinfecdis.8b00275
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Bacterial tRNA modification synthesis pathways are critical to cell survival under stress and thus represent ideal mechanism-based targets for antibiotic development. One such target is the tRNA-(N 1 G37) methyltransferase (TrmD), which is conserved and essential in many bacterial pathogens. Here we developed and applied a widely applicable, radioactivity-free, bioluminescence-based high-throughput screen (HTS) against 116350 compounds from structurally diverse small-molecule libraries to identify inhibitors of Pseudomonas aeruginosa TrmD ( PaTrmD). Of 285 compounds passing primary and secondary screens, a total of 61 TrmD inhibitors comprised of more than 12 different chemical scaffolds were identified, all showing submicromolar to low micromolar enzyme inhibitor constants, with binding affinity confirmed by thermal stability and surface plasmon resonance. S-Adenosyl-l-methionine (SAM) competition assays suggested that compounds in the pyridine-pyrazole-piperidine scaffold were substrate SAM-competitive inhibitors. This was confirmed in structural studies, with nuclear magnetic resonance analysis and crystal structures of PaTrmD showing pyridine-pyrazole-piperidine compounds bound in the SAM-binding pocket. Five hits showed cellular activities against Gram-positive bacteria, including mycobacteria, while one compound, a SAM-noncompetitive inhibitor, exhibited broad-spectrum antibacterial activity. The results of this HTS expand the repertoire of TrmD-inhibiting molecular scaffolds that show promise for antibiotic development.

  • Organizational Affiliation

    Antimicrobial Resistance Interdisciplinary Research Group , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (guanine-N(1)-)-methyltransferase
A, B
269Pseudomonas aeruginosa UCBPP-PA14Mutation(s): 0 
Gene Names: trmD
Find proteins for Q02RL6 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore Q02RL6 
Go to UniProtKB:  Q02RL6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02RL6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM (Subject of Investigation/LOI)
Query on SAM

Download Ideal Coordinates CCD File 
C15 H22 N6 O5 S
9WO (Subject of Investigation/LOI)
Query on 9WO

Download Ideal Coordinates CCD File 
D [auth B]N-{(3S)-1-[3-(pyridin-4-yl)-1H-pyrazol-5-yl]piperidin-3-yl}-1H-indole-2-carboxamide
C22 H22 N6 O
Experimental Data & Validation

Experimental Data

  • Resolution: 2.75 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.184 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.02α = 90
b = 86.02β = 90
c = 149.191γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Foundation (Singapore)SingaporeING137070-BIO
Ministry of Education (Singapore)SingaporeRG154/14
Ministry of Education (Singapore)SingaporeMOE2015-T2-2-075

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description