4UFW

Plasmodium vivax N-myristoyltransferase in complex with a pyridyl inhibitor (compound 22)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1039/c5md00242g
  • Primary Citation of Related Structures:  

  • 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 inh ...

    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.


    Organizational Affiliation

    Department of Chemistry , Imperial College London , London , SW7 2AZ , UK . Email: e.tate@imperial.ac.uk ; Tel: +44 (0)2075 943 752.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
A, B, C
385Plasmodium vivax (strain Salvador I)Mutation(s): 0 
EC: 2.3.1.97
Find proteins for A5K1A2 (Plasmodium vivax (strain Salvador I))
Go to UniProtKB:  A5K1A2
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NHW
Query on NHW

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Download CCD File 
A, B, C
2-oxopentadecyl-CoA
C36 H64 N7 O17 P3 S
JKWHUJMJVNMKEF-UOCZADIYSA-J
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A, B, C
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
7Y6
Query on 7Y6

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Download CCD File 
A, B, C
4-chloranyl-N-[2-(3-methoxyphenyl)ethanimidoyl]-2-piperidin-4-yloxy-benzamide
C21 H24 Cl N3 O3
LWKDHLRBDHZTMF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.520α = 90.00
b = 121.910β = 90.00
c = 178.800γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-04-20
    Type: Database references