6QDF

Leishmania major N-myristoyltransferase in complex with thienopyrimidine inhibitor IMP-0000096


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Novel Thienopyrimidine Inhibitors of Leishmania N -Myristoyltransferase with On-Target Activity in Intracellular Amastigotes.

Bell, A.S.Yu, Z.Hutton, J.A.Wright, M.H.Brannigan, J.A.Paape, D.Roberts, S.M.Sutherell, C.L.Ritzefeld, M.Wilkinson, A.J.Smith, D.F.Leatherbarrow, R.J.Tate, E.W.

(2020) J Med Chem 63: 7740-7765

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00570
  • Primary Citation of Related Structures:  
    6QD9, 6QDA, 6QDB, 6QDC, 6QDD, 6QDE, 6QDF, 6QDG, 6QDH

  • PubMed Abstract: 

    The leishmaniases, caused by Leishmania species of protozoan parasites, are neglected tropical diseases with millions of cases worldwide. Current therapeutic approaches are limited by toxicity, resistance, and cost. N -Myristoyltransferase (NMT), an enzyme ubiquitous and essential in all eukaryotes, has been validated via genetic and pharmacological methods as a promising anti-leishmanial target. Here we describe a comprehensive structure-activity relationship (SAR) study of a thienopyrimidine series previously identified in a high-throughput screen against Leishmania NMT, across 68 compounds in enzyme- and cell-based assay formats. Using a chemical tagging target engagement biomarker assay, we identify the first inhibitor in this series with on-target NMT activity in leishmania parasites. Furthermore, crystal structure analyses of 12 derivatives in complex with Leishmania major NMT revealed key factors important for future structure-guided optimization delivering IMP-105 ( 43 ), a compound with modest activity against Leishmania donovani intracellular amastigotes and excellent selectivity (>660-fold) for Leishmania NMT over human NMTs.


  • Organizational Affiliation

    Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, U.K. W12 0BZ.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycylpeptide N-tetradecanoyltransferase421Leishmania majorMutation(s): 0 
Gene Names: NMTLMJF_32_0080
EC: 2.3.1.97
UniProt
Find proteins for Q4Q5S8 (Leishmania major)
Explore Q4Q5S8 
Go to UniProtKB:  Q4Q5S8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4Q5S8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MYA
Query on MYA

Download Ideal Coordinates CCD File 
B [auth A]TETRADECANOYL-COA
C35 H62 N7 O17 P3 S
DUAFKXOFBZQTQE-QSGBVPJFSA-N
HWN
Query on HWN

Download Ideal Coordinates CCD File 
D [auth A]3-[[6-tert-butyl-2-[methyl-[(3S)-1-methylpyrrolidin-3-yl]amino]thieno[3,2-d]pyrimidin-4-yl]-methyl-amino]propanenitrile
C20 H30 N6 S
IIIBKWKCKFKYOT-AWEZNQCLSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.519α = 90
b = 90.286β = 111.83
c = 53.01γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references
  • Version 2.0: 2023-09-13
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary