5G22

Plasmodium vivax N-myristoyltransferase in complex with a quinoline inhibitor (compound 26)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


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

  • 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: [email protected] ; Email: [email protected].


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
A, B, C
385Plasmodium vivaxMutation(s): 0 
EC: 2.3.1.97
UniProt
Find proteins for A5K1A2 (Plasmodium vivax (strain Salvador I))
Explore A5K1A2 
Go to UniProtKB:  A5K1A2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5K1A2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NHW
Query on NHW
Download Ideal Coordinates CCD File 
D [auth A],
I [auth B],
M [auth C]		2-oxopentadecyl-CoA
C36 H64 N7 O17 P3 S
JKWHUJMJVNMKEF-UOCZADIYSA-J
YN4
Query on YN4
Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
N [auth C]		ETHYL 4-[(2-CYANOETHYL)SULFANYL]-6-{[6-(PIPERAZIN-1-YL)
C25 H27 N5 O3 S
BOXNSEIJTUHQDY-UHFFFAOYSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL
Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
P [auth C]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG
Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.97α = 90
b = 123.36β = 90
c = 179.37γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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