Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 8 (3-[(2-thienylthio)methyl]benzoic acid)

Experimental Data Snapshot

  • Resolution: 3.06 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.193 

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This is version 1.3 of the entry. See complete history


Fragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification.

Thomas, S.E.Whitehouse, A.J.Brown, K.Burbaud, S.Belardinelli, J.M.Sangen, J.Lahiri, R.Libardo, M.D.J.Gupta, P.Malhotra, S.Boshoff, H.I.M.Jackson, M.Abell, C.Coyne, A.G.Blundell, T.L.Floto, R.A.Mendes, V.

(2020) Nucleic Acids Res 48: 8099-8112

  • DOI: https://doi.org/10.1093/nar/gkaa539
  • Primary Citation of Related Structures:  
    6NVR, 6NW6, 6NW7, 6QO2, 6QO3, 6QO4, 6QO6, 6QOA, 6QOC, 6QOD, 6QOE, 6QOF, 6QOG, 6QOH, 6QOI, 6QOJ, 6QOK, 6QOL, 6QOM, 6QON, 6QOO, 6QOP, 6QOQ, 6QOR, 6QOS, 6QOT, 6QOU, 6QOV, 6QOW, 6QOX, 6QQS, 6QQX, 6QQY, 6QR5, 6QR6, 6QR8

  • PubMed Abstract: 

    Translational frameshift errors are often deleterious to the synthesis of functional proteins and could therefore be promoted therapeutically to kill bacteria. TrmD (tRNA-(N(1)G37) methyltransferase) is an essential tRNA modification enzyme in bacteria that prevents +1 errors in the reading frame during protein translation and represents an attractive potential target for the development of new antibiotics. Here, we describe the application of a structure-guided fragment-based drug discovery approach to the design of a new class of inhibitors against TrmD in Mycobacterium abscessus. Fragment library screening, followed by structure-guided chemical elaboration of hits, led to the rapid development of drug-like molecules with potent in vitro TrmD inhibitory activity. Several of these compounds exhibit activity against planktonic M. abscessus and M. tuberculosis as well as against intracellular M. abscessus and M. leprae, indicating their potential as the basis for a novel class of broad-spectrum mycobacterial drugs.

  • Organizational Affiliation

    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (guanine-N(1)-)-methyltransferase
A, B
244Mycobacteroides abscessusMutation(s): 0 
Gene Names: trmDMAB_3226c
Find proteins for B1MDI3 (Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CCUG 20993 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 / L948))
Explore B1MDI3 
Go to UniProtKB:  B1MDI3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1MDI3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on JBB

Download Ideal Coordinates CCD File 
C [auth B]3-(thiophen-2-ylsulfanylmethyl)benzoic acid
C12 H10 O2 S2
Experimental Data & Validation

Experimental Data

  • Resolution: 3.06 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.596α = 90
b = 79.739β = 90
c = 86.758γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other privateUnited KingdomCystic Fibrosis Trust Registered Charity No. (England and Wales) 1079049, Registered Charity No. (Scotland) SC040196

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references
  • Version 1.2: 2020-08-26
    Changes: Database references
  • Version 1.3: 2024-05-15
    Changes: Advisory, Data collection, Database references