4UFW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

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:  
    4UFV, 4UFW, 4UFX

  • 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 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE ABC385Plasmodium vivaxMutation(s): 0 
EC: 2.3.1.97
Find proteins for A5K1A2 (Plasmodium vivax (strain Salvador I))
Explore A5K1A2 
Go to UniProtKB:  A5K1A2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NHW
Query on NHW

Download Ideal Coordinates CCD File 
A, B, C
2-oxopentadecyl-CoA
C36 H64 N7 O17 P3 S
JKWHUJMJVNMKEF-UOCZADIYSA-J
 Ligand Interaction
7Y6
Query on 7Y6

Download Ideal Coordinates 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
SO4
Query on SO4

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

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

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

Download Ideal Coordinates CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.52α = 90
b = 121.91β = 90
c = 178.8γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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