Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51.81 kDa 
• Atom Count: 3653 
• Modelled Residue Count: 402 
• Deposited Residue Count: 438 
• Unique protein chains: 1

5AG6

CRYSTAL STRUCTURE OF LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE (NMT) WITH BOUND MYRISTOYL-COA AND A THIAZOLIDINONE LIGAND

• PDB DOI: 10.2210/pdb5AG6/pdb

• Classification: TRANSFERASE
• Organism(s): Leishmania major
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-01-29 Released: 2015-10-07 
• Deposition Author(s): Robinson, D.A., Spinks, D., Smith, V.C., Thompson, S., Smith, A., Torrie, L.S., McElroy, S.P., Brand, S., Brenk, R., Frearson, J.A., Read, K.D., Wyatt, P.G., Gilbert, I.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.236 
• R-Value Work: 0.172 
• R-Value Observed: 0.175 

Literature

Development of Small-Molecule Trypanosoma Brucei N-Myristoyltransferase Inhibitors: Discovery and Optimisation of a Novel Binding Mode.

Spinks, D., Smith, V., Thompson, S., Robinson, D.A., Luksch, T., Smith, A., Torrie, L.S., Mcelroy, S., Stojanovski, L., Norval, S., Collie, I.T., Hallyburton, I., Rao, B., Brand, S., Brenk, R., Frearson, J.A., Read, K.D., Wyatt, P.G., Gilbert, I.H.

(2015) ChemMedChem 10: 1821

• PubMed: 26395087 
• DOI: 10.1002/cmdc.201500301
• Primary Citation of Related Structures:  
  5AG4, 5AG5, 5AG6, 5AG7, 5AGE


• PubMed Abstract: 
  

The enzyme N-myristoyltransferase (NMT) from Trypanosoma brucei has been validated both chemically and biologically as a potential drug target for human African trypanosomiasis. We previously reported the development of some very potent compounds based around a pyrazole sulfonamide series, derived from a high-throughput screen. Herein we describe work around thiazolidinone and benzomorpholine scaffolds that were also identified in the screen. An X-ray crystal structure of the thiazolidinone hit in Leishmania major NMT showed the compound bound in the previously reported active site, utilising a novel binding mode. This provides potential for further optimisation. The benzomorpholinone was also found to bind in a similar region. Using an X-ray crystallography/structure-based design approach, the benzomorpholinone series was further optimised, increasing activity against T. brucei NMT by >1000-fold. A series of trypanocidal compounds were identified with suitable in vitro DMPK properties, including CNS exposure for further development. Further work is required to increase selectivity over the human NMT isoform and activity against T. brucei.

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Organizational Affiliation: 

Drug Discovery Unit, College of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, UK. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE	A	438	Leishmania major	Mutation(s): 0  Gene Names: NMT, LMJF_32_0080 EC: 2.3.1.97
UniProt
Find proteins for Q4Q5S8 (Leishmania major) Explore Q4Q5S8  Go to UniProtKB:  Q4Q5S8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYA	C [auth A]	TETRADECANOYL-COA C35 H62 N7 O17 P3 S DUAFKXOFBZQTQE-GLTUGWJXDB
5PE	B [auth A]	(2R)-2-(4-hydroxy-3-methoxyphenyl)-3-(pyridin-2-ylmethyl)-1,3-thiazolidin-4-one C16 H16 N2 O3 S HHJAKBZAUFYRBJ-MRXNPFEDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.236 
• R-Value Work: 0.172 
• R-Value Observed: 0.175 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.72	α = 90
b = 90.27	β = 114.57
c = 53.27	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-01-29 
• Released Date: 2015-10-07 
Deposition Author(s): Robinson, D.A., Spinks, D., Smith, V.C., Thompson, S., Smith, A., Torrie, L.S., McElroy, S.P., Brand, S., Brenk, R., Frearson, J.A., Read, K.D., Wyatt, P.G., Gilbert, I.H.

Revision History  

• Version 1.0: 2015-10-07
  Type: Initial release
  
• Version 1.1: 2015-11-11
  Changes: Database references