6QQW

Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


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Literature

Development of Inhibitors againstMycobacterium abscessustRNA (m1G37) Methyltransferase (TrmD) Using Fragment-Based Approaches.

Whitehouse, A.J.Thomas, S.E.Brown, K.P.Fanourakis, A.Chan, D.S.Libardo, M.D.J.Mendes, V.Boshoff, H.I.M.Floto, R.A.Abell, C.Blundell, T.L.Coyne, A.G.

(2019) J Med Chem 62: 7210-7232

  • DOI: 10.1021/acs.jmedchem.9b00809
  • Primary Citation of Related Structures:  
    6QR0, 6QQQ, 6QR2, 6QR1, 6QR4, 6QQR, 6QR3, 6QQU, 6QQT, 6QRG, 6QRB, 6QRA, 6QRD, 6QRC, 6QRF, 6QRE, 6QQW, 6QQV, 6QR7, 6QR9, 6QQZ

  • PubMed Abstract: 
  • Mycobacterium abscessus ( Mab ) is a rapidly growing species of multidrug-resistant nontuberculous mycobacteria that has emerged as a growing threat to individuals with cystic fibrosis and other pre-existing chronic lung diseases. Mab pulmonary infections are difficult, or sometimes impossible, to treat and result in accelerated lung function decline and premature death ...

    Mycobacterium abscessus ( Mab ) is a rapidly growing species of multidrug-resistant nontuberculous mycobacteria that has emerged as a growing threat to individuals with cystic fibrosis and other pre-existing chronic lung diseases. Mab pulmonary infections are difficult, or sometimes impossible, to treat and result in accelerated lung function decline and premature death. There is therefore an urgent need to develop novel antibiotics with improved efficacy. tRNA (m 1 G37) methyltransferase (TrmD) is a promising target for novel antibiotics. It is essential in Mab and other mycobacteria, improving reading frame maintenance on the ribosome to prevent frameshift errors. In this work, a fragment-based approach was employed with the merging of two fragments bound to the active site, followed by structure-guided elaboration to design potent nanomolar inhibitors against Mab TrmD. Several of these compounds exhibit promising activity against mycobacterial species, including Mycobacterium tuberculosis and Mycobacterium leprae in addition to Mab , supporting the use of TrmD as a target for the development of antimycobacterial compounds.


    Organizational Affiliation

    Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA (guanine-N(1)-)-methyltransferaseA, B244Mycobacteroides abscessusMutation(s): 0 
Gene Names: trmDMAB_3226c
EC: 2.1.1.228
UniProt
Find proteins for B1MDI3 (Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543))
Explore B1MDI3 
Go to UniProtKB:  B1MDI3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JDQ (Subject of Investigation/LOI)
Query on JDQ

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]3-[1-(phenylmethyl)indol-6-yl]-1~{H}-pyrazol-5-amine
C18 H16 N4
IXGUTMYAJBKSPV-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
JDQ Binding MOAD:  6QQW Kd: 1.90e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.52α = 90
b = 77.97β = 90
c = 86.5γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



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: 2019-09-18
    Type: Initial release