4BBH

Plasmodium vivax N-myristoyltransferase with a bound benzothiophene inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4BBH/pdb

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


• Deposited: 2012-09-23 Released: 2012-12-05 
• Deposition Author(s): Rackham, M.D., Brannigan, J.A., Moss, D.K., Yu, Z., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.264 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 

Literature

Discovery of Novel and Ligand-Efficient Inhibitors of Plasmodium Falciparum and Plasmodium Vivax N-Myristoyltransferase.

Rackham, M.D., Brannigan, J.A., Moss, D.K., Yu, Z., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

(2013) J Med Chem 56: 371

• PubMed: 23170970 
• DOI: https://doi.org/10.1021/jm301474t
• Primary Citation of Related Structures:  
  4BBH


• PubMed Abstract: 
  

  N-Myristoyltransferase (NMT) is an attractive antiprotozoan drug target. A lead-hopping approach was utilized in the design and synthesis of novel benzo[b]thiophene-containing inhibitors of Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) NMT. These inhibitors are selective against Homo sapiens NMT1 (HsNMT), have excellent ligand efficiency (LE), and display antiparasitic activity in vitro. The binding mode of this series was determined by crystallography and shows a novel binding mode for the benzothiophene ring.

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Organizational Affiliation: 

Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K.

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: 139.52 kDa 
• Atom Count: 10,684 
• Modelled Residue Count: 1,135 
• 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHW	E [auth A], K [auth B], P [auth C]	2-oxopentadecyl-CoA C36 H64 N7 O17 P3 S JKWHUJMJVNMKEF-UOCZADIYSA-J
YBN	F [auth A], L [auth B], Q [auth C]	3-methoxybenzyl 3-(piperidin-4-yloxy)-1-benzothiophene-2-carboxylate C22 H23 N O4 S GEVWCNOQZDSSIG-UHFFFAOYSA-N
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	D [auth A], J [auth B], O [auth C]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	H [auth A], M [auth B], R [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	I [auth A], N [auth B], S [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
YBN	PDBBind:  4BBH	Ki: 80 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.264 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.47	α = 90
b = 121.87	β = 90
c = 178.34	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-05 
Deposition Author(s): Rackham, M.D., Brannigan, J.A., Moss, D.K., Yu, Z., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

Revision History  

• Version 1.0: 2012-12-05
  Type: Initial release
  
• Version 1.1: 2013-01-23
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other