5AG7 | pdb_00005ag7

CRYSTAL STRUCTURE OF LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE (NMT) WITH BOUND MYRISTOYL-COA AND A BENZOMORPHOLINE LIGAND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.266 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.177 (Depositor) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5AG7

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Development of Small-Molecule Trypanosoma Brucei N-Myristoyltransferase Inhibitors: Discovery and Optimisation of a Novel Binding Mode.

Spinks, D.Smith, V.Thompson, S.Robinson, D.A.Luksch, T.Smith, A.Torrie, L.S.Mcelroy, S.Stojanovski, L.Norval, S.Collie, I.T.Hallyburton, I.Rao, B.Brand, S.Brenk, R.Frearson, J.A.Read, K.D.Wyatt, P.G.Gilbert, I.H.

(2015) ChemMedChem 10: 1821

  • DOI: https://doi.org/10.1002/cmdc.201500301
  • Primary Citation Related Structures: 
    5AG4, 5AG5, 5AG6, 5AG7, 5AGE

  • PubMed Abstract: 

    The enzyme N-myristoyltransferase (NMT) from Trypanosoma brucei has been validated both chemically and biologically as a potential drug target for human African trypanosomiasis. We previously reported the development of some very potent compounds based around a pyrazole sulfonamide series, derived from a high-throughput screen. Herein we describe work around thiazolidinone and benzomorpholine scaffolds that were also identified in the screen. An X-ray crystal structure of the thiazolidinone hit in Leishmania major NMT showed the compound bound in the previously reported active site, utilising a novel binding mode. This provides potential for further optimisation. The benzomorpholinone was also found to bind in a similar region. Using an X-ray crystallography/structure-based design approach, the benzomorpholinone series was further optimised, increasing activity against T. brucei NMT by >1000-fold. A series of trypanocidal compounds were identified with suitable in vitro DMPK properties, including CNS exposure for further development. Further work is required to increase selectivity over the human NMT isoform and activity against T. brucei.


  • Organizational Affiliation
    • Drug Discovery Unit, College of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, UK.

Macromolecule Content 

  • Total Structure Weight: 51.73 kDa 
  • Atom Count: 3,519 
  • Modeled Residue Count: 411 
  • Deposited Residue Count: 438 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE438Leishmania majorMutation(s): 0 
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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MYA

Query on MYA



Download:Ideal Coordinates CCD File
C [auth A]TETRADECANOYL-COA
C35 H62 N7 O17 P3 S
DUAFKXOFBZQTQE-QSGBVPJFSA-N
XXL

Query on XXL



Download:Ideal Coordinates CCD File
B [auth A]ethyl (3-oxo-2,3-dihydro-4H-1,4-benzoxazin-4-yl)acetate
C12 H13 N O4
PNKJMWWGWBCNQL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.266 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.177 (Depositor) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.241α = 90
b = 91.216β = 113.69
c = 53.229γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2015-11-11
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description