4UFV

Plasmodium vivax N-myristoyltransferase in complex with a pyridyl inhibitor (compound 18)

• PDB DOI: https://doi.org/10.2210/pdb4UFV/pdb

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


• Deposited: 2015-03-19 Released: 2016-02-03 
• Deposition Author(s): Yu, Z., Brannigan, J.A., Rangachari, K., Heal, W.P., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.237 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

Literature

Discovery of Pyridyl-Based Inhibitors of Plasmodium Falciparum N-Myristoyltransferase

Yu, Z., Brannigan, J.A., Rangachari, K., Heal, W.P., Wilkinson, A.J., Holder, A.A., Leatherbarrow, R.J., Tate, E.W.

(2015) Medchemcomm 6: 1767

• PubMed: 26962430 
• DOI: https://doi.org/10.1039/c5md00242g
• Primary Citation of Related Structures:  
  4UFV, 4UFW, 4UFX


• PubMed Abstract: 
  

  N -Myristoyltransferase (NMT) represents an attractive drug target in parasitic infections such as malaria due to its genetic essentiality and amenability to inhibition by drug-like small molecules. Scaffold simplification from previously reported inhibitors containing bicyclic cores identified phenyl derivative 3 , providing a versatile platform to study the effects of substitution on the scaffold, which yielded pyridyl 19 . This molecule exhibited improved enzyme and cellular potency, and reduced lipophilicity compared to inhibitor 3 . Further structure-based inhibitor design led to the discovery of 30 , the most potent inhibitor in this series, which showed single-digit nM enzyme affinity and sub-μM anti-plasmodial activity.

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Organizational Affiliation: 

Department of Chemistry , Imperial College London , London , SW7 2AZ , UK . Email: [e-mail] ; Tel: [phone].

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: 139.97 kDa 
• Atom Count: 11,339 
• Modelled Residue Count: 1,142 
• 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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHW	D [auth A], J [auth B], P [auth C]	2-oxopentadecyl-CoA C36 H64 N7 O17 P3 S JKWHUJMJVNMKEF-UOCZADIYSA-J
31A	E [auth A], K [auth B], Q [auth C]	N-[2-(3-methoxyphenyl)ethanimidoyl]-2-piperidin-4-yloxy-benzamide C21 H25 N3 O3 WTWXRFGIIFJWMN-UHFFFAOYSA-N
SO4	L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	H [auth A], I [auth A], O [auth B], T [auth C]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
GOA	U [auth C]	GLYCOLIC ACID C2 H4 O3 AEMRFAOFKBGASW-UHFFFAOYSA-N
CL	G [auth A], N [auth B], S [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	F [auth A], M [auth B], R [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.237 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.48	α = 90
b = 118.99	β = 90
c = 177.74	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Yu, Z., Brannigan, J.A., Rangachari, K., Heal, W.P., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

Revision History  

• Version 1.0: 2016-02-03
  Type: Initial release
  
• Version 1.1: 2016-04-20
  Changes: Database references
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other