4B11

Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 13)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

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 Anti-Malarial 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-TETRADECANOYLTRANSFERASEA, B, C385Plasmodium 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 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NHW
Query on NHW

Download Ideal Coordinates CCD File 
E [auth A], K [auth B], P [auth C]2-oxopentadecyl-CoA
C36 H64 N7 O17 P3 S
JKWHUJMJVNMKEF-UOCZADIYSA-J
 Ligand Interaction
7I1
Query on 7I1

Download Ideal Coordinates CCD File 
D [auth A], J [auth B], O [auth C]3-methyl-N-(naphthalen-1-ylmethyl)-4-piperidin-4-yloxy-1-benzofuran-2-carboxamide
C26 H26 N2 O3
JDZKIYVLMLQBQF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
F [auth A], L [auth B], Q [auth C]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A], M [auth B], R [auth C], T [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A], N [auth B], S [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7I1IC50 :  2300   nM  PDBBind
7I1IC50:  2300   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.34α = 90
b = 119.03β = 90
c = 175.47γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
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