4A30 | pdb_00004a30

CRYSTAL STRUCTURE OF LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE (NMT) WITH BOUND MYRISTOYL-COA AND A PYRAZOLE SULPHONAMIDE LIGAND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.221 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of a novel class of orally active trypanocidal N-myristoyltransferase inhibitors.

Brand, S.Cleghorn, L.A.McElroy, S.P.Robinson, D.A.Smith, V.C.Hallyburton, I.Harrison, J.R.Norcross, N.R.Spinks, D.Bayliss, T.Norval, S.Stojanovski, L.Torrie, L.S.Frearson, J.A.Brenk, R.Fairlamb, A.H.Ferguson, M.A.Read, K.D.Wyatt, P.G.Gilbert, I.H.

(2012) J Med Chem 55: 140-152

  • DOI: https://doi.org/10.1021/jm201091t
  • Primary Citation of Related Structures:  
    4A2Z, 4A30, 4A31, 4A32, 4A33

  • PubMed Abstract: 

    N-Myristoyltransferase (NMT) represents a promising drug target for human African trypanosomiasis (HAT), which is caused by the parasitic protozoa Trypanosoma brucei. We report the optimization of a high throughput screening hit (1) to give a lead molecule DDD85646 (63), which has potent activity against the enzyme (IC(50) = 2 nM) and T. brucei (EC(50) = 2 nM) in culture. The compound has good oral pharmacokinetics and cures rodent models of peripheral HAT infection. This compound provides an excellent tool for validation of T. brucei NMT as a drug target for HAT as well as a valuable lead for further optimization.


  • 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.

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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.221 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.636α = 90
b = 90.676β = 114.02
c = 53.514γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-21
    Type: Initial release
  • Version 1.1: 2012-01-25
    Changes: Other
  • Version 1.2: 2018-02-14
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description