5T6C

Crystal structure of Aspergillus fumigatus N-myristoyl transferase in complex with myristoyl CoA and a dichloro-methylpyridinyl-methoxy-phenyl-pyridine piperazine ligand

• PDB DOI: https://doi.org/10.2210/pdb5T6C/pdb

• Classification: TRANSFERASE
• Organism(s): Aspergillus fumigatus Af293
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-01 Released: 2017-09-13 
• Deposition Author(s): Robinson, D.A., Wyatt, P.G.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.256 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 

Starting Model: experimental

Literature

Design and Synthesis of Brain Penetrant Trypanocidal N-Myristoyltransferase Inhibitors.

Bayliss, T., Robinson, D.A., Smith, V.C., Brand, S., McElroy, S.P., Torrie, L.S., Mpamhanga, C., Norval, S., Stojanovski, L., Brenk, R., Frearson, J.A., Read, K.D., Gilbert, I.H., Wyatt, P.G.

(2017) J Med Chem 60: 9790-9806

• PubMed: 29125744 
• DOI: https://doi.org/10.1021/acs.jmedchem.7b01255
• Primary Citation of Related Structures:  
  5T5U, 5T6C, 5T6E, 5T6H


• PubMed Abstract: 
  

  N-Myristoyltransferase (NMT) represents a promising drug target within the parasitic protozoa Trypanosoma brucei (T. brucei), the causative agent for human African trypanosomiasis (HAT) or sleeping sickness. We have previously validated T. brucei NMT as a promising druggable target for the treatment of HAT in both stages 1 and 2 of the disease. We report on the use of the previously reported DDD85646 (1) as a starting point for the design of a class of potent, brain penetrant inhibitors of T. brucei NMT.

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Organizational Affiliation: 

Drug Discovery Unit, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.85 kDa 
• Atom Count: 3,779 
• Modelled Residue Count: 392 
• Deposited Residue Count: 411 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycylpeptide N-tetradecanoyltransferase	A	411	Aspergillus fumigatus Af293	Mutation(s): 0  Gene Names: nmt1, AFUA_4G08070 EC: 2.3.1.97
UniProt
Find proteins for Q9UVX3 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore Q9UVX3  Go to UniProtKB:  Q9UVX3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYA	B [auth A]	TETRADECANOYL-COA C35 H62 N7 O17 P3 S DUAFKXOFBZQTQE-QSGBVPJFSA-N
75S	C [auth A]	1-(4-{3,5-dichloro-4-[(2-methylpyridin-3-yl)methoxy]phenyl}pyridin-2-yl)piperazine C22 H22 Cl2 N4 O KDTZTRFMUYKFDT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.256 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.143	α = 90
b = 58.599	β = 90
c = 152.146	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-09-13 
Deposition Author(s): Robinson, D.A., Wyatt, P.G.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	WT077705
Wellcome Trust	United Kingdom	WT094090

Revision History  

• Version 1.0: 2017-09-13
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Database references
• Version 1.2: 2017-12-27
  Changes: Database references
• Version 1.3: 2019-06-12
  Changes: Data collection, Structure summary
• Version 1.4: 2024-01-17
  Changes: Data collection, Database references, Refinement description