4CGO

Leishmania major N-myristoyltransferase in complex with a thienopyrimidine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Diverse Modes of Binding in Structures of Leishmania Major N-Myristoyltransferase with Selective Inhibitors

Brannigan, J.A.Roberts, S.M.Bell, A.S.Hutton, J.A.Hodgkinson, M.R.Tate, E.W.Leatherbarrow, R.J.Smith, D.F.Wilkinson, A.J.

(2014) Iucrj 1: 250

  • DOI: 10.1107/S2052252514013001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The leishmaniases are a spectrum of global diseases of poverty associated with immune dysfunction and are the cause of high morbidity. Despite the long history of these diseases, no effective vaccine is available and the currently used drugs are vari ...

    The leishmaniases are a spectrum of global diseases of poverty associated with immune dysfunction and are the cause of high morbidity. Despite the long history of these diseases, no effective vaccine is available and the currently used drugs are variously compromised by moderate efficacy, complex side effects and the emergence of resistance. It is therefore widely accepted that new therapies are needed. N-Myristoyltransferase (NMT) has been validated pre-clinically as a target for the treatment of fungal and parasitic infections. In a previously reported high-throughput screening program, a number of hit compounds with activity against NMT from Leishmania donovani have been identified. Here, high-resolution crystal structures of representative compounds from four hit series in ternary complexes with myristoyl-CoA and NMT from the closely related L. major are reported. The structures reveal that the inhibitors associate with the peptide-binding groove at a site adjacent to the bound myristoyl-CoA and the catalytic α-carboxylate of Leu421. Each inhibitor makes extensive apolar contacts as well as a small number of polar contacts with the protein. Remarkably, the compounds exploit different features of the peptide-binding groove and collectively occupy a substantial volume of this pocket, suggesting that there is potential for the design of chimaeric inhibitors with significantly enhanced binding. Despite the high conservation of the active sites of the parasite and human NMTs, the inhibitors act selectively over the host enzyme. The role of conformational flexibility in the side chain of Tyr217 in conferring selectivity is discussed.


    Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
A
411Leishmania majorMutation(s): 0 
Gene Names: NMT
EC: 2.3.1.97
Find proteins for Q4Q5S8 (Leishmania major)
Go to UniProtKB:  Q4Q5S8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYA
Query on MYA

Download SDF File 
Download CCD File 
A
TETRADECANOYL-COA
MYRISTOYL-COA
C35 H62 N7 O17 P3 S
DUAFKXOFBZQTQE-GLTUGWJXDB
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
6KV
Query on 6KV

Download SDF File 
Download CCD File 
A
3-[methyl-[2-[methyl-(1-methylpiperidin-4-yl)amino]thieno[3,2-d]pyrimidin-4-yl]amino]propanenitrile
C17 H24 N6 S
JVWILFYYJUGFPA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6KVIC50: 299 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.813α = 90.00
b = 90.628β = 111.91
c = 53.200γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-08-13
    Type: Database references