5T6E

Crystal structure of Aspergillus fumigatus N-myristoyl transferase in complex with myristoyl CoA and a dichloro-dimethylpyridyl-methoxy-phenyl-pyridyl-piperazine ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Design and Synthesis of Brain Penetrant Trypanocidal N-Myristoyltransferase Inhibitors.

Bayliss, T.Robinson, D.A.Smith, V.C.Brand, S.McElroy, S.P.Torrie, L.S.Mpamhanga, C.Norval, S.Stojanovski, L.Brenk, R.Frearson, J.A.Read, K.D.Gilbert, I.H.Wyatt, P.G.

(2017) J Med Chem 60: 9790-9806

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b01255
  • Primary Citation of Related Structures:  
    5T5U, 5T6C, 5T6E, 5T6H

  • PubMed Abstract: 

    N-Myristoyltransferase (NMT) represents a promising drug target within the parasitic protozoa Trypanosoma brucei (T. brucei), the causative agent for human African trypanosomiasis (HAT) or sleeping sickness. We have previously validated T. brucei NMT as a promising druggable target for the treatment of HAT in both stages 1 and 2 of the disease. We report on the use of the previously reported DDD85646 (1) as a starting point for the design of a class of potent, brain penetrant inhibitors of T. brucei NMT.


  • Organizational Affiliation

    Drug Discovery Unit, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycylpeptide N-tetradecanoyltransferase411Aspergillus fumigatus Af293Mutation(s): 0 
Gene Names: nmt1AFUA_4G08070
EC: 2.3.1.97
UniProt
Find proteins for Q9UVX3 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293))
Explore Q9UVX3 
Go to UniProtKB:  Q9UVX3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UVX3
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 
B [auth A]TETRADECANOYL-COA
C35 H62 N7 O17 P3 S
DUAFKXOFBZQTQE-QSGBVPJFSA-N
75R
Query on 75R

Download Ideal Coordinates CCD File 
C [auth A]1-(4-{3,5-dichloro-4-[(2,4-dimethylpyridin-3-yl)methoxy]phenyl}pyridin-2-yl)piperazine
C23 H24 Cl2 N4 O
UBIXTVHUCALUIC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.276α = 90
b = 58.339β = 90
c = 152.1γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomWT077705
Wellcome TrustUnited KingdomWT094090

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Database references
  • Version 1.2: 2017-12-27
    Changes: Database references
  • Version 1.3: 2019-06-12
    Changes: Data collection, Structure summary
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description