4B13

Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 25)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Design and Synthesis of Inhibitors of Plasmodium Falciparum N-Myristoyltransferase, a Promising Target for Antimalarial Drug Discovery.

Yu, Z.Brannigan, J.A.Moss, D.K.Brzozowski, A.M.Wilkinson, A.J.Holder, A.A.Tate, E.W.Leatherbarrow, R.J.

(2012) J Med Chem 55: 8879

  • DOI: 10.1021/jm301160h
  • Primary Citation of Related Structures:  
    4B13, 4B14, 4B10, 4B11, 4B12

  • PubMed Abstract: 
  • Design of inhibitors for N-myristoyltransferase (NMT), an enzyme responsible for protein trafficking in Plasmodium falciparum , the most lethal species of parasites that cause malaria, is described. Chemistry-driven optimization of compound 1 from a focused NMT inhibitor library led to the identification of two early lead compounds 4 and 25, which showed good enzyme and cellular potency and excellent selectivity over human NMT ...

    Design of inhibitors for N-myristoyltransferase (NMT), an enzyme responsible for protein trafficking in Plasmodium falciparum , the most lethal species of parasites that cause malaria, is described. Chemistry-driven optimization of compound 1 from a focused NMT inhibitor library led to the identification of two early lead compounds 4 and 25, which showed good enzyme and cellular potency and excellent selectivity over human NMT. These molecules provide a valuable starting point for further development.


    Organizational Affiliation

    Department of Chemistry, Imperial College London, London SW7 2AZ, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE ABC385Plasmodium vivaxMutation(s): 0 
EC: 2.3.1.97
Find proteins for A5K1A2 (Plasmodium vivax (strain Salvador I))
Explore A5K1A2 
Go to UniProtKB:  A5K1A2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NHW
Query on NHW

Download Ideal Coordinates CCD File 
A, B, C
2-oxopentadecyl-CoA
C36 H64 N7 O17 P3 S
JKWHUJMJVNMKEF-UOCZADIYSA-J
 Ligand Interaction
X25
Query on X25

Download Ideal Coordinates CCD File 
A, B, C
4-{[2-(3-benzyl-1,2,4-oxadiazol-5-yl)-3-methyl-1-benzofuran-4-yl]oxy}piperidine
C23 H23 N3 O3
QVBWWXFSCCHYFK-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
X25IC50 :  2000   nM  PDBBind
X25IC50:  2000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.32α = 90
b = 119.13β = 90
c = 178.46γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2012-11-07
    Changes: Database references