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 6GNV | pdb_00006gnv

Crystal Structure of Leishmania major N-Myristoyltransferase (NMT) With Bound Myristoyl-CoA and a isopropyl methyl indole aryl sulphonamide ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.208 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 
    0.156 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6GNV

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

Literature

A Molecular Hybridization Approach for the Design of Potent, Highly Selective, and Brain-Penetrant N-Myristoyltransferase Inhibitors.

Harrison, J.R., Brand, S., Smith, V., Robinson, D.A., Thompson, S., Smith, A., Davies, K., Mok, N., Torrie, L.S., Collie, I., Hallyburton, I., Norval, S., Simeons, F.R.C., Stojanovski, L., Frearson, J.A., Brenk, R., Wyatt, P.G., Gilbert, I.H., Read, K.D.

(2018) J Med Chem 61: 8374-8389

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00884
  • Primary Citation Related Structures: 
    6GNH, 6GNS, 6GNT, 6GNU, 6GNV

  • PubMed Abstract: 

    Crystallography has guided the hybridization of two series of Trypanosoma brucei N-myristoyltransferase (NMT) inhibitors, leading to a novel highly selective series. The effect of combining the selectivity enhancing elements from two pharmacophores is shown to be additive and has led to compounds that have greater than 1000-fold selectivity for TbNMT vs HsNMT. Further optimization of the hybrid series has identified compounds with significant trypanocidal activity capable of crossing the blood-brain barrier. By using CF-1 mdr1a deficient mice, we were able to demonstrate full cures in vivo in a mouse model of stage 2 African sleeping sickness. This and previous work provides very strong validation for NMT as a drug target for human African trypanosomiasis in both the peripheral and central nervous system stages of disease.


  • Organizational Affiliation: 
    • Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences , University of Dundee , Dundee , DD1 5EH , United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 48.83 kDa 
  • Atom Count: 3,673 
  • Modeled Residue Count: 411 
  • Deposited Residue Count: 411 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycylpeptide N-tetradecanoyltransferase411Leishmania majorMutation(s): 0 
Gene Names: NMT, LMJF_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
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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
F5E

Query on F5E



Download:Ideal Coordinates CCD File
C [auth A]~{N}-[2-methyl-5-(2-methylpropyl)indazol-4-yl]-4-[4-(1-methylpiperidin-4-yl)butyl]benzenesulfonamide
C28 H40 N4 O2 S
HAEBJCXYCZWIGA-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.208 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 0.156 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.7α = 90
b = 90.42β = 114.83
c = 53.68γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata 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
Wellcome TrustUnited KingdomWT083481

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary