4A95

Plasmodium vivax N-myristoyltransferase with quinoline inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Plasmodium Vivax N-Myristoyltransferase Inhibitors: Screening, Synthesis, and Structural Characterization of Their Binding Mode.

Goncalves, V.Brannigan, J.A.Whalley, D.Ansell, K.H.Saxty, B.Holder, A.A.Wilkinson, A.J.Tate, E.W.Leatherbarrow, R.J.

(2012) J.Med.Chem. 55: 3578

  • DOI: 10.1021/jm300040p

  • PubMed Abstract: 
  • N-Myristoyltransferase (NMT) is a prospective drug target against parasitic protozoa. Herein we report the successful discovery of a series of Plasmodium vivax NMT inhibitors by high-throughput screening. A high-resolution crystal structure of the hi ...

    N-Myristoyltransferase (NMT) is a prospective drug target against parasitic protozoa. Herein we report the successful discovery of a series of Plasmodium vivax NMT inhibitors by high-throughput screening. A high-resolution crystal structure of the hit compound in complex with NMT was obtained, allowing understanding of its novel binding mode. A set of analogues was designed and tested to define the chemical groups relevant for activity and selectivity.


    Organizational Affiliation

    Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
A, B, C
384Plasmodium vivax (strain Salvador I)EC: 2.3.1.97
Find proteins for A5K1A2 (Plasmodium vivax (strain Salvador I))
Go to UniProtKB:  A5K1A2
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NHW
Query on NHW

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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 
B
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
9MT
Query on 9MT

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Download CCD File 
A, B, C
3-(3-BUTYL-6-METHOXY-2-METHYL-QUINOLIN-4-YL)SULFANYLPROPANENITRILE
C18 H22 N2 O S
UJFIVLIFWNFOIZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9MTIC50: 2900 nM BINDINGMOAD
9MTKi: 1730 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.490α = 90.00
b = 121.560β = 90.00
c = 179.010γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2012-07-18
    Type: Atomic model, Derived calculations, Non-polymer description, Refinement description