4CAE

Plasmodium vivax N-myristoyltransferase in complex with a benzothiophene inhibitor (compound 20b)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design and Synthesis of High Affinity Inhibitors of Plasmodium Falciparum and Plasmodium Vivax N-Myristoyltransferases Directed by Ligand Efficiency Dependent Lipophilicity (Lelp).

Rackham, M.D.Brannigan, J.A.Rangachari, K.Meister, S.Wilkinson, A.J.Holder, A.A.Leatherbarrow, R.J.Tate, E.W.

(2014) J.Med.Chem. 57: 2773

  • DOI: 10.1021/jm500066b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N-Myristoyltransferase (NMT) is an essential eukaryotic enzyme and an attractive drug target in parasitic infections such as malaria. We have previously reported that 2-(3-(piperidin-4-yloxy)benzo[b]thiophen-2-yl)-5-((1,3,5-trimethyl-1H-pyrazol-4-yl) ...

    N-Myristoyltransferase (NMT) is an essential eukaryotic enzyme and an attractive drug target in parasitic infections such as malaria. We have previously reported that 2-(3-(piperidin-4-yloxy)benzo[b]thiophen-2-yl)-5-((1,3,5-trimethyl-1H-pyrazol-4-yl)methyl)-1,3,4-oxadiazole (34c) is a high affinity inhibitor of both Plasmodium falciparum and P. vivax NMT and displays activity in vivo against a rodent malaria model. Here we describe the discovery of 34c through optimization of a previously described series. Development, guided by targeting a ligand efficiency dependent lipophilicity (LELP) score of less than 10, yielded a 100-fold increase in enzyme affinity and a 100-fold drop in lipophilicity with the addition of only two heavy atoms. 34c was found to be equipotent on chloroquine-sensitive and -resistant cell lines and on both blood and liver stage forms of the parasite. These data further validate NMT as an exciting drug target in malaria and support 34c as an attractive tool for further optimization.


    Organizational Affiliation

    Department of Chemistry, Imperial College London , London SW7 2AZ, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
A, B, C
384Plasmodium vivax (strain Salvador I)Mutation(s): 0 
EC: 2.3.1.97
Find proteins for A5K1A2 (Plasmodium vivax (strain Salvador I))
Go to UniProtKB:  A5K1A2
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NHW
Query on NHW

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A, B, C
2-oxopentadecyl-CoA
C36 H64 N7 O17 P3 S
JKWHUJMJVNMKEF-UOCZADIYSA-J
 Ligand Interaction
SO4
Query on SO4

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B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
3F3
Query on 3F3

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Download CCD File 
A, B, C
4-[(2-{5-[(3-METHOXYPHENYL)METHYL]-1,3,4-OXADIAZOL-2-YL}-1-BENZOTHIOPHEN-3-YL)OXY]PIPERIDINE
C23 H23 N3 O3 S
RWKJYYGODHUKPP-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A, B, C
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3F3Ki: 18 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.501α = 90.00
b = 121.054β = 90.00
c = 178.677γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-04-09
    Type: Database references