4UWI | pdb_00004uwi

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.231 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4UWI

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 48.5 kDa 
  • Atom Count: 3,683 
  • Modeled Residue Count: 391 
  • Deposited Residue Count: 407 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE407Aspergillus fumigatusMutation(s): 0 
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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UVX3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MYA

Query on MYA



Download:Ideal Coordinates CCD File
C [auth A]TETRADECANOYL-COA
C35 H62 N7 O17 P3 S
DUAFKXOFBZQTQE-QSGBVPJFSA-N
XMQ

Query on XMQ



Download:Ideal Coordinates CCD File
B [auth A]2,6-dichloro-4-[3-(4-methylpiperazin-1-yl)propyl]-N-(1,3,5-trimethyl-1H-pyrazol-4-yl)benzenesulfonamide
C20 H29 Cl2 N5 O2 S
REQUPDWBGITKAD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.231 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.789α = 90
b = 56.897β = 90
c = 141.607γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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: 2015-01-14
    Changes: Database references
  • Version 1.2: 2018-02-14
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other