4A95

Plasmodium vivax N-myristoyltransferase with quinoline inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4A95/pdb

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


• Deposited: 2011-11-24 Released: 2012-06-27 
• Deposition Author(s): Goncalves, V., Brannigan, J.A., Whalley, D., Ansell, K.H., Saxty, B., Holder, A.A., Wilkinson, A.J., Tate, E.W., Leatherbarrow, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.236 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

Starting Model: other

Literature

Discovery of Plasmodium Vivax N-Myristoyltransferase Inhibitors: Screening, Synthesis, and Structural Characterization of Their Binding Mode.

Goncalves, V., Brannigan, J.A., Whalley, D., Ansell, K.H., Saxty, B., Holder, A.A., Wilkinson, A.J., Tate, E.W., Leatherbarrow, R.J.

(2012) J Med Chem 55: 3578

• PubMed: 22439843 
• DOI: https://doi.org/10.1021/jm300040p
• Primary Citation of Related Structures:  
  4A95


• PubMed Abstract: 
  

  N-Myristoyltransferase (NMT) is a prospective drug target against parasitic protozoa. Herein we report the successful discovery of a series of Plasmodium vivax NMT inhibitors by high-throughput screening. A high-resolution crystal structure of the hit compound in complex with NMT was obtained, allowing understanding of its novel binding mode. A set of analogues was designed and tested to define the chemical groups relevant for activity and selectivity.

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Organizational Affiliation: 

Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 139.03 kDa 
• Atom Count: 11,498 
• Modelled Residue Count: 1,134 
• Deposited Residue Count: 1,152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE	A, B, C	384	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
9MT	D [auth A], H [auth B], M [auth C]	3-(3-BUTYL-6-METHOXY-2-METHYL-QUINOLIN-4-YL)SULFANYLPROPANENITRILE C18 H22 N2 O S UJFIVLIFWNFOIZ-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
9MT	PDBBind:  4A95	Ki: 1730 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.236 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.49	α = 90
b = 121.56	β = 90
c = 179.01	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-27 
Deposition Author(s): Goncalves, V., Brannigan, J.A., Whalley, D., Ansell, K.H., Saxty, B., Holder, A.A., Wilkinson, A.J., Tate, E.W., Leatherbarrow, R.J.

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 1.1: 2012-07-18
  Changes: Atomic model, Derived calculations, Non-polymer description, Refinement description
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description