4B13

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

• PDB DOI: https://doi.org/10.2210/pdb4B13/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium vivax
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-07-06 Released: 2012-10-17 
• Deposition Author(s): Yu, Z., Brannigan, J.A., Moss, D.K., Brzozowski, A.M., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

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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 

Starting Model: experimental

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

• PubMed: 23035716 
• DOI: https://doi.org/10.1021/jm301160h
• Primary Citation of Related Structures:  
  4B10, 4B11, 4B12, 4B13, 4B14


• 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. These molecules provide a valuable starting point for further development.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 139.65 kDa 
• Atom Count: 11,104 
• Modelled Residue Count: 1,138 
• Deposited Residue Count: 1,155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE	A, B, C	385	Plasmodium vivax	Mutation(s): 0  EC: 2.3.1.97
UniProt
Find proteins for A5K1A2 (Plasmodium vivax (strain Salvador I)) Explore A5K1A2  Go to UniProtKB:  A5K1A2

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHW	E [auth A], I [auth B], N [auth C]	2-oxopentadecyl-CoA C36 H64 N7 O17 P3 S JKWHUJMJVNMKEF-UOCZADIYSA-J
X25	D [auth A], H [auth B], M [auth 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
SO4	J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	F [auth A], K [auth B], O [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	G [auth A], L [auth B], P [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
X25	PDBBind:  4B13	IC50: 2000 (nM) from 1 assay(s)

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 = 57.32	α = 90
b = 119.13	β = 90
c = 178.46	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-17 
Deposition Author(s): Yu, Z., Brannigan, J.A., Moss, D.K., Brzozowski, A.M., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2012-11-07
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description