5G1Z

Plasmodium vivax N-myristoyltransferase in complex with a quinoline inhibitor (compound 1)

• PDB DOI: https://doi.org/10.2210/pdb5G1Z/pdb

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


• Deposited: 2016-04-06 Released: 2017-02-15 
• Deposition Author(s): Goncalves, V., Brannigan, J.A., Laporte, A., Bell, A.S., Roberts, S.M., Wilkinson, A.J., Leatherbarrow, R.J., Tate, E.W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.187 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 

Literature

Structure-guided optimization of quinoline inhibitors of Plasmodium N-myristoyltransferase.

Goncalves, V., Brannigan, J.A., Laporte, A., Bell, A.S., Roberts, S.M., Wilkinson, A.J., Leatherbarrow, R.J., Tate, E.W.

(2017) Medchemcomm 8: 191-197

• PubMed: 28626547 
• DOI: https://doi.org/10.1039/c6md00531d
• Primary Citation of Related Structures:  
  5G1Z, 5G20, 5G21, 5G22


• PubMed Abstract: 
  

  The parasite Plasmodium vivax is the most widely distributed cause of recurring malaria. N -Myristoyltransferase (NMT), an enzyme that catalyses the covalent attachment of myristate to the N-terminal glycine of substrate proteins, has been described as a potential target for the treatment of this disease. Herein, we report the synthesis and the structure-guided optimization of a series of quinolines with balanced activity against both Plasmodium vivax and Plasmodium falciparum N -myristoyltransferase (NMT).

---

Organizational Affiliation: 

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

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: 139.79 kDa 
• Atom Count: 11,889 
• Modelled Residue Count: 1,140 
• 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHW	D [auth A], K [auth B], P [auth C]	2-oxopentadecyl-CoA C36 H64 N7 O17 P3 S JKWHUJMJVNMKEF-UOCZADIYSA-J
U53	E [auth A], L [auth B], Q [auth C]	ethyl 4-(2-cyanoethylsulfanyl)-6-methoxy-quinoline-3-carboxylate C16 H16 N2 O3 S TZDUQSHGGUOAJU-UHFFFAOYSA-N
SO4	H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	F [auth A], M [auth B], R [auth C], S [auth C]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	J [auth A], O [auth B], U [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	G [auth A], N [auth B], T [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.187 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.4	α = 90
b = 118.9	β = 90
c = 175.3	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-15 
Deposition Author(s): Goncalves, V., Brannigan, J.A., Laporte, A., Bell, A.S., Roberts, S.M., Wilkinson, A.J., Leatherbarrow, R.J., Tate, E.W.

Revision History  

• Version 1.0: 2017-02-15
  Type: Initial release
  
• Version 1.1: 2017-06-28
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other