2WSA

Crystal Structure of Leishmania major N-myristoyltransferase (NMT) with bound myristoyl-CoA and a pyrazole sulphonamide ligand (DDD85646)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

N-Myristoyltransferase Inhibitors as New Leads to Treat Sleeping Sickness.

Frearson, J.A.Brand, S.Cleghorn, L.A.T.Mcelroy, S.Smid, O.Stojanovski, L.Torrie, L.Robinson, D.A.Hallyburton, I.Guther, M.L.Price, H.P.Mpamhanga, C.P.Brannigan, J.A.Hodgkinson, M.Raimi, O.Van Aalten, D.M.F.Brenk, R.Gilbert, I.H.Read, K.D.Fairlamb, A.H.Ferguson, M.A.J.Smith, D.F.Wyatt, P.G.

(2010) Nature 464: 728

  • DOI: https://doi.org/10.1038/nature08893
  • Primary Citation of Related Structures:  
    2WSA, 3H5Z

  • PubMed Abstract: 

    African sleeping sickness or human African trypanosomiasis, caused by Trypanosoma brucei spp., is responsible for approximately 30,000 deaths each year. Available treatments for this disease are poor, with unacceptable efficacy and safety profiles, particularly in the late stage of the disease when the parasite has infected the central nervous system. Here we report the validation of a molecular target and the discovery of associated lead compounds with the potential to address this lack of suitable treatments. Inhibition of this target-T. brucei N-myristoyltransferase-leads to rapid killing of trypanosomes both in vitro and in vivo and cures trypanosomiasis in mice. These high-affinity inhibitors bind into the peptide substrate pocket of the enzyme and inhibit protein N-myristoylation in trypanosomes. The compounds identified have promising pharmaceutical properties and represent an opportunity to develop oral drugs to treat this devastating disease. Our studies validate T. brucei N-myristoyltransferase as a promising therapeutic target for human African trypanosomiasis.


  • Organizational Affiliation

    Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE438Leishmania majorMutation(s): 0 
EC: 2.3.1.97
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MYA
Query on MYA

Download Ideal Coordinates CCD File 
B [auth A]TETRADECANOYL-COA
C35 H62 N7 O17 P3 S
DUAFKXOFBZQTQE-QSGBVPJFSA-N
646
Query on 646

Download Ideal Coordinates CCD File 
C [auth A]2,6-dichloro-4-(2-piperazin-1-ylpyridin-4-yl)-N-(1,3,5-trimethyl-1H-pyrazol-4-yl)benzenesulfonamide
C21 H24 Cl2 N6 O2 S
XMBSZPZJLPTFMV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
646 BindingDB:  2WSA Ki: min: 8.4, max: 41 (nM) from 3 assay(s)
IC50: 2 (nM) from 1 assay(s)
Binding MOAD:  2WSA Kd: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.51α = 90
b = 90.317β = 112.27
c = 52.972γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-23
    Type: Initial release
  • Version 1.1: 2011-10-12
    Changes: Advisory, Atomic model, Derived calculations, Version format compliance
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description