4CYN

Leishmania major N-myristoyltransferase in complex with an aminoacylpyrrolidine inhibitor (2b)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-Based Design of Potent and Selective Leishmania N- Myristoyltransferase Inhibitors.

Hutton, J.A.Goncalves, V.Brannigan, J.A.Paape, D.Wright, M.H.Waugh, T.M.Roberts, S.M.Bell, A.S.Wilkinson, A.J.Smith, D.F.Leatherbarrow, R.J.Tate, E.W.

(2014) J Med Chem 57: 8664

  • DOI: 10.1021/jm5011397
  • Primary Citation of Related Structures:  
    4CYN, 4CYO, 4CYP, 4CYQ

  • PubMed Abstract: 
  • Inhibitors of Leishmania N-myristoyltransferase (NMT), a potential target for the treatment of leishmaniasis, obtained from a high-throughput screen, were resynthesized to validate activity. Crystal structures bound to Leishmania major NMT were obtained, and the active diastereoisomer of one of the inhibitors was identified ...

    Inhibitors of Leishmania N-myristoyltransferase (NMT), a potential target for the treatment of leishmaniasis, obtained from a high-throughput screen, were resynthesized to validate activity. Crystal structures bound to Leishmania major NMT were obtained, and the active diastereoisomer of one of the inhibitors was identified. On the basis of structural insights, enzyme inhibition was increased 40-fold through hybridization of two distinct binding modes, resulting in novel, highly potent Leishmania donovani NMT inhibitors with good selectivity over the human enzyme.


    Organizational Affiliation

    Department of Chemistry, Imperial College London , London SW7 2AZ, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASEA411Leishmania 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYA
Query on MYA

Download Ideal Coordinates CCD File 
D [auth A]TETRADECANOYL-COA
C35 H62 N7 O17 P3 S
DUAFKXOFBZQTQE-GLTUGWJXDB
 Ligand Interaction
A6M
Query on A6M

Download Ideal Coordinates CCD File 
C [auth A](3R)-3-amino-4-(4-chlorophenyl)-1-[(3R,4S)-3-(4-chlorophenyl)-4-(hydroxymethyl)pyrrolidin-1-yl]butan-1-one
C21 H24 Cl2 N2 O2
ZFSKJGRASNTEBX-DBVUQKKJSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
A6M Binding MOAD:  4CYN Ki: 1406 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.668α = 90
b = 91.638β = 111.82
c = 53.163γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-01
    Type: Initial release
  • Version 1.1: 2014-11-05
    Changes: Database references