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

Experimental Data Snapshot

  • Resolution: 1.54 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

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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: https://doi.org/10.1021/acs.jmedchem.8b00884
  • Primary Citation of Related Structures:  
    6GNH, 6GNS, 6GNT, 6GNU, 6GNV

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycylpeptide N-tetradecanoyltransferase438Leishmania majorMutation(s): 0 
Gene Names: NMTLMJF_32_0080
Find proteins for Q4Q5S8 (Leishmania major)
Explore Q4Q5S8 
Go to UniProtKB:  Q4Q5S8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4Q5S8
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
F5Z (Subject of Investigation/LOI)
Query on F5Z

Download Ideal Coordinates CCD File 
C [auth A]4-[4-(1-methylpiperidin-4-yl)butyl]-~{N}-[6-(2-methylpropyl)quinolin-5-yl]benzenesulfonamide
C29 H39 N3 O2 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.54 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.309α = 90
b = 89.934β = 114.74
c = 52.884γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description