4C7H

Leismania major N-myristoyltransferase in complex with a peptidomimetic (-NH2) molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Peptidomimetic Inhibitors of N-Myristoyltransferase from Human Malaria and Leishmaniasis Parasites.

Olaleye, T.O.Brannigan, J.A.Roberts, S.M.Leatherbarrow, R.J.Wilkinson, A.J.Tate, E.W.

(2014) Org Biomol Chem 12: 8132

  • DOI: 10.1039/c4ob01669f
  • Primary Citation of Related Structures:  
    4C68, 4C7H, 4C7I

  • PubMed Abstract: 
  • N-Myristoyltransferase (NMT) has been shown to be essential in Leishmania and subsequently validated as a drug target in Plasmodium. Herein, we discuss the use of antifungal NMT inhibitors as a basis for inhibitor development resulting in the first sub-micromolar peptidomimetic inhibitors of Plasmodium and Leishmania NMTs ...

    N-Myristoyltransferase (NMT) has been shown to be essential in Leishmania and subsequently validated as a drug target in Plasmodium. Herein, we discuss the use of antifungal NMT inhibitors as a basis for inhibitor development resulting in the first sub-micromolar peptidomimetic inhibitors of Plasmodium and Leishmania NMTs. High-resolution structures of these inhibitors with Plasmodium and Leishmania NMTs permit a comparative analysis of binding modes, and provide the first crystal structure evidence for a ternary NMT-Coenzyme A/myristoylated peptide product complex.


    Organizational Affiliation

    Department of Chemistry, Imperial College London, London, SW7 2AZ, UK. e.tate@imperial.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYA (Subject of Investigation/LOI)
Query on MYA

Download Ideal Coordinates CCD File 
E [auth A]TETRADECANOYL-COA
C35 H62 N7 O17 P3 S
DUAFKXOFBZQTQE-GLTUGWJXDB
 Ligand Interaction
COA (Subject of Investigation/LOI)
Query on COA

Download Ideal Coordinates CCD File 
D [auth A]COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
ENF (Subject of Investigation/LOI)
Query on ENF

Download Ideal Coordinates CCD File 
F [auth A]N-{(5E)-10-[(9E)-tetradec-9-enoylamino]dec-5-enoyl}-L-seryl-N-(2-cyclohexylethyl)-L-lysinamide
C41 H79 N5 O5
QIQBRVNLNJERKS-FBKDKWTRSA-N
 Ligand Interaction
EN5 (Subject of Investigation/LOI)
Query on EN5

Download Ideal Coordinates CCD File 
C [auth A]N-(10-aminodecanoyl)-L-seryl-N-(2-cyclohexylethyl)-L-lysinamide
C27 H53 N5 O4
OVRFOVZVAWIPDE-ZEQRLZLVSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
G [auth A], H [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.659α = 90
b = 91.131β = 113.85
c = 53.777γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2014-10-08
    Changes: Database references