5G20

Leishmania major N-myristoyltransferase in complex with a quinoline inhibitor (compound 19).

• PDB DOI: https://doi.org/10.2210/pdb5G20/pdb

• Classification: TRANSFERASE
• Organism(s): Leishmania major
• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.219 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

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).

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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)

Macromolecule Content

• Total Structure Weight: 49 kDa 
• Atom Count: 3,990 
• Modelled Residue Count: 411 
• Deposited Residue Count: 411 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE	A	411	Leishmania major	Mutation(s): 0  EC: 2.3.1.97
UniProt
Find proteins for Q4Q5S8 (Leishmania major) Explore Q4Q5S8  Go to UniProtKB:  Q4Q5S8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYA	C [auth A]	TETRADECANOYL-COA C35 H62 N7 O17 P3 S DUAFKXOFBZQTQE-QSGBVPJFSA-N
QBY	D [auth A]	6-(BENZYLOXY)-4-(ETHYLSULFANYL)-3-[(MORPHOLIN-4-YL) C23 H24 N2 O3 S INDSTSRQMXNXSG-UHFFFAOYSA-N
DMS	E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.219 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.718	α = 90
b = 90.651	β = 112.72
c = 52.913	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