Crystal structure of Aspergillus fumigatus N-myristoyl transferase in complex with myristoyl CoA and a capped pyrazole sulphonamide ligand

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

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Lead optimization of a pyrazole sulfonamide series of Trypanosoma brucei N-myristoyltransferase inhibitors: identification and evaluation of CNS penetrant compounds as potential treatments for stage 2 human African trypanosomiasis.

Brand, S.Norcross, N.R.Thompson, S.Harrison, J.R.Smith, V.C.Robinson, D.A.Torrie, L.S.McElroy, S.P.Hallyburton, I.Norval, S.Scullion, P.Stojanovski, L.Simeons, F.R.van Aalten, D.Frearson, J.A.Brenk, R.Fairlamb, A.H.Ferguson, M.A.Wyatt, P.G.Gilbert, I.H.Read, K.D.

(2014) J Med Chem 57: 9855-9869

  • DOI: https://doi.org/10.1021/jm500809c
  • Primary Citation of Related Structures:  
    4UWI, 4UWJ

  • PubMed Abstract: 

    Trypanosoma brucei N-myristoyltransferase (TbNMT) is an attractive therapeutic target for the treatment of human African trypanosomiasis (HAT). From previous studies, we identified pyrazole sulfonamide, DDD85646 (1), a potent inhibitor of TbNMT. Although this compound represents an excellent lead, poor central nervous system (CNS) exposure restricts its use to the hemolymphatic form (stage 1) of the disease. With a clear clinical need for new drug treatments for HAT that address both the hemolymphatic and CNS stages of the disease, a chemistry campaign was initiated to address the shortfalls of this series. This paper describes modifications to the pyrazole sulfonamides which markedly improved blood-brain barrier permeability, achieved by reducing polar surface area and capping the sulfonamide. Moreover, replacing the core aromatic with a flexible linker significantly improved selectivity. This led to the discovery of DDD100097 (40) which demonstrated partial efficacy in a stage 2 (CNS) mouse model of HAT.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Find proteins for Q9UVX3 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293))
Explore Q9UVX3 
Go to UniProtKB:  Q9UVX3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UVX3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MYA

Download Ideal Coordinates CCD File 
C35 H62 N7 O17 P3 S
Query on 7L5

Download Ideal Coordinates CCD File 
B [auth A]2,6-dichloro-N-(difluoromethyl)-4-[3-(piperidin-4-yl)propyl]-N-(1,3,5-trimethyl-1H-pyrazol-4-yl)benzenesulfonamide
C21 H28 Cl2 F2 N4 O2 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.013α = 90
b = 58.608β = 90
c = 152.366γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2016-01-27
    Changes: Database references
  • Version 1.3: 2018-02-14
    Changes: Database references
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other