4MCC

HinTrmD in complex with N-[4-(AMINOMETHYL)BENZYL]-4-OXO-3,4-DIHYDROTHIENO[2,3-D]PYRIMIDINE-5-CARBOXAMIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Selective Inhibitors of Bacterial t-RNA-(N(1)G37) Methyltransferase (TrmD) That Demonstrate Novel Ordering of the Lid Domain.

Hill, P.J.Abibi, A.Albert, R.Andrews, B.Gagnon, M.M.Gao, N.Grebe, T.Hajec, L.I.Huang, J.Livchak, S.Lahiri, S.D.McKinney, D.C.Thresher, J.Wang, H.Olivier, N.Buurman, E.T.

(2013) J.Med.Chem. 56: 7278-7288

  • DOI: 10.1021/jm400718n
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The tRNA-(N(1)G37) methyltransferase (TrmD) is essential for growth and highly conserved in both Gram-positive and Gram-negative bacterial pathogens. Additionally, TrmD is very distinct from its human orthologue TRM5 and thus is a suitable target for ...

    The tRNA-(N(1)G37) methyltransferase (TrmD) is essential for growth and highly conserved in both Gram-positive and Gram-negative bacterial pathogens. Additionally, TrmD is very distinct from its human orthologue TRM5 and thus is a suitable target for the design of novel antibacterials. Screening of a collection of compound fragments using Haemophilus influenzae TrmD identified inhibitory, fused thieno-pyrimidones that were competitive with S-adenosylmethionine (SAM), the physiological methyl donor substrate. Guided by X-ray cocrystal structures, fragment 1 was elaborated into a nanomolar inhibitor of a broad range of Gram-negative TrmD isozymes. These compounds demonstrated no activity against representative human SAM utilizing enzymes, PRMT1 and SET7/9. This is the first report of selective, nanomolar inhibitors of TrmD with demonstrated ability to order the TrmD lid in the absence of tRNA.


    Organizational Affiliation

    Departments of Chemistry, ‡Biosciences and §Discovery Sciences, Infection Innovative Medicines Unit, AstraZeneca R&D Boston , 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA (guanine-N(1)-)-methyltransferase
A, B
246Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)Mutation(s): 0 
Gene Names: trmD
EC: 2.1.1.228
Find proteins for P43912 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Go to UniProtKB:  P43912
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
21X
Query on 21X

Download SDF File 
Download CCD File 
A, B
N-[4-(aminomethyl)benzyl]-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide
C15 H14 N4 O2 S
ZOJIHHOGTNVURO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
21XIC50: 560 nM BINDINGMOAD
21XIC50: 560 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.181 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 74.272α = 90.00
b = 74.272β = 90.00
c = 119.135γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PROCESSdata reduction
BUSTERrefinement
SPECdata collection
AMoREphasing
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-10-09
    Type: Database references