6QDF | pdb_00006qdf

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 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6QDF

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 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.

Macromolecule Content 

  • Total Structure Weight: 49.96 kDa 
  • Atom Count: 4,038 
  • Modeled Residue Count: 411 
  • Deposited Residue Count: 421 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
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