8APT | pdb_00008apt

Crystal Structure of H. influenzae TrmD in complex with Compound 13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.179 (Depositor), 0.179 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.161 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Evaluating the druggability of TrmD, a potential antibacterial target, through design and microbiological profiling of a series of potent TrmD inhibitors.

Wilkinson, A.J.Ooi, N.Finlayson, J.Lee, V.E.Lyth, D.Maskew, K.S.Newman, R.Orr, D.Ansell, K.Birchall, K.Canning, P.Coombs, P.Fusani, L.McIver, E.Pisco, J.Ireland, P.M.Jenkins, C.Norville, I.H.Southern, S.J.Cowan, R.Hall, G.Kettleborough, C.Savage, V.J.Cooper, I.R.

(2023) Bioorg Med Chem Lett 90: 129331-129331

  • DOI: https://doi.org/10.1016/j.bmcl.2023.129331
  • Primary Citation Related Structures: 
    8APT, 8APU, 8APV, 8APW

  • PubMed Abstract: 

    The post-transcriptional modifier tRNA-(N 1 G37) methyltransferase (TrmD) has been proposed to be essential for growth in many Gram-negative and Gram-positive pathogens, however previously reported inhibitors show only weak antibacterial activity. In this work, optimisation of fragment hits resulted in compounds with low nanomolar TrmD inhibition incorporating features designed to enhance bacterial permeability and covering a range of physicochemical space. The resulting lack of significant antibacterial activity suggests that whilst TrmD is highly ligandable, its essentiality and druggability are called into question.


  • Organizational Affiliation
    • Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield SK10 4TG, UK. Electronic address: Andrew.Wilkinson@infextx.com.

Macromolecule Content 

  • Total Structure Weight: 30.2 kDa 
  • Atom Count: 2,400 
  • Modeled Residue Count: 248 
  • Deposited Residue Count: 266 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
tRNA (guanine-N(1)-)-methyltransferase266Haemophilus influenzaeMutation(s): 0 
Gene Names: trmDCGSHiGG_03625
EC: 2.1.1.228
UniProt
Find proteins for A5UG04 (Haemophilus influenzae (strain PittGG))
Explore A5UG04 
Go to UniProtKB:  A5UG04
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5UG04
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NN9
(Subject of Investigation/LOI)

Query on NN9



Download:Ideal Coordinates CCD File
B [auth A]6-[[3-(aminomethyl)phenyl]methylamino]pyridine-3-carboxamide
C14 H16 N4 O
WXURPGONLMDDHC-UHFFFAOYSA-N
CIT

Query on CIT



Download:Ideal Coordinates CCD File
C [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.179 (Depositor), 0.179 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.161 (DCC) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.671α = 90
b = 94.671β = 90
c = 177.958γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
StructureStudiodata collection
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description