Crystal structure of TrmD from Mycobacterium tuberculosis in complex with active-site inhibitor

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report

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Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-N1)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism.

Zhong, W.Pasunooti, K.K.Balamkundu, S.Wong, Y.H.Nah, Q.Gadi, V.Gnanakalai, S.Chionh, Y.H.McBee, M.E.Gopal, P.Lim, S.H.Olivier, N.Buurman, E.T.Dick, T.Liu, C.F.Lescar, J.Dedon, P.C.

(2019) J Med Chem 62: 7788-7805

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00582
  • Primary Citation of Related Structures:  
    5ZHI, 5ZHJ, 5ZHK, 5ZHL, 5ZHM, 5ZHN, 6JOE, 6JOF

  • PubMed Abstract: 

    Among the >120 modified ribonucleosides in the prokaryotic epitranscriptome, many tRNA modifications are critical to bacterial survival, which makes their synthetic enzymes ideal targets for antibiotic development. Here we performed a structure-based design of inhibitors of tRNA-(N 1 G37) methyltransferase, TrmD, which is an essential enzyme in many bacterial pathogens. On the basis of crystal structures of TrmDs from Pseudomonas aeruginosa and Mycobacterium tuberculosis , we synthesized a series of thienopyrimidinone derivatives with nanomolar potency against TrmD in vitro and discovered a novel active site conformational change triggered by inhibitor binding. This tyrosine-flipping mechanism is uniquely found in P. aeruginosa TrmD and renders the enzyme inaccessible to the cofactor S -adenosyl-l-methionine (SAM) and probably to the substrate tRNA. Biophysical and biochemical structure-activity relationship studies provided insights into the mechanisms underlying the potency of thienopyrimidinones as TrmD inhibitors, with several derivatives found to be active against Gram-positive and mycobacterial pathogens. These results lay a foundation for further development of TrmD inhibitors as antimicrobial agents.

  • Organizational Affiliation

    Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , 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)-)-methyltransferase238Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: trmD
Find proteins for P9WFY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFY7 
Go to UniProtKB:  P9WFY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFY7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BWR (Subject of Investigation/LOI)
Query on BWR

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[[4-[(4-azanylpiperidin-1-yl)methyl]phenyl]methyl]-4-oxidanylidene-3~{H}-thieno[2,3-d]pyrimidine-5-carboxamide
C20 H23 N5 O2 S
Binding Affinity Annotations 
IDSourceBinding Affinity
BWR BindingDB:  6JOF Kd: 1.04e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.07α = 90
b = 51.38β = 90.19
c = 57.95γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Foundation (Singapore)Singapore--

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description