6GNV

Crystal Structure of Leishmania major N-Myristoyltransferase (NMT) With Bound Myristoyl-CoA and a isopropyl methyl indole aryl sulphonamide ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A Molecular Hybridization Approach for the Design of Potent, Highly Selective, and Brain-Penetrant N-Myristoyltransferase Inhibitors.

Harrison, J.R.Brand, S.Smith, V.Robinson, D.A.Thompson, S.Smith, A.Davies, K.Mok, N.Torrie, L.S.Collie, I.Hallyburton, I.Norval, S.Simeons, F.R.C.Stojanovski, L.Frearson, J.A.Brenk, R.Wyatt, P.G.Gilbert, I.H.Read, K.D.

(2018) J. Med. Chem. 61: 8374-8389

  • DOI: 10.1021/acs.jmedchem.8b00884
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystallography has guided the hybridization of two series of Trypanosoma brucei N-myristoyltransferase (NMT) inhibitors, leading to a novel highly selective series. The effect of combining the selectivity enhancing elements from two pharmacophores i ...

    Crystallography has guided the hybridization of two series of Trypanosoma brucei N-myristoyltransferase (NMT) inhibitors, leading to a novel highly selective series. The effect of combining the selectivity enhancing elements from two pharmacophores is shown to be additive and has led to compounds that have greater than 1000-fold selectivity for TbNMT vs HsNMT. Further optimization of the hybrid series has identified compounds with significant trypanocidal activity capable of crossing the blood-brain barrier. By using CF-1 mdr1a deficient mice, we were able to demonstrate full cures in vivo in a mouse model of stage 2 African sleeping sickness. This and previous work provides very strong validation for NMT as a drug target for human African trypanosomiasis in both the peripheral and central nervous system stages of disease.


    Organizational Affiliation

    Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences , University of Dundee , Dundee , DD1 5EH , United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycylpeptide N-tetradecanoyltransferase
A
411Leishmania majorMutation(s): 0 
Gene Names: NMT
EC: 2.3.1.97
Find proteins for Q4Q5S8 (Leishmania major)
Go to UniProtKB:  Q4Q5S8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYA
Query on MYA

Download SDF File 
Download CCD File 
A
TETRADECANOYL-COA
MYRISTOYL-COA
C35 H62 N7 O17 P3 S
DUAFKXOFBZQTQE-GLTUGWJXDB
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
F5E
Query on F5E

Download SDF File 
Download CCD File 
A
~{N}-[2-methyl-5-(2-methylpropyl)indazol-4-yl]-4-[4-(1-methylpiperidin-4-yl)butyl]benzenesulfonamide
C28 H40 N4 O2 S
HAEBJCXYCZWIGA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.152 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.700α = 90.00
b = 90.420β = 114.83
c = 53.680γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
SCALAdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomWT077705
Wellcome TrustUnited KingdomWT094090
Wellcome TrustUnited KingdomWT083481

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release