6NXG | pdb_00006nxg

Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor 303a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.174 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.149 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.150 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6NXG

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Identification of Selective Inhibitors ofPlasmodiumN-Myristoyltransferase by High-Throughput Screening.

Harupa, A.De Las Heras, L.Colmenarejo, G.Lyons-Abbott, S.Reers, A.Caballero Hernandez, I.Chung, C.W.Charter, D.Myler, P.J.Fernandez-Menendez, R.M.Calderon, F.Palomo, S.Rodriguez, B.Berlanga, M.Herreros-Aviles, E.Staker, B.L.Fernandez Alvaro, E.Kaushansky, A.

(2020) J Med Chem 63: 591-600

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01343
  • Primary Citation Related Structures: 
    6NXG

  • PubMed Abstract: 

    New drugs that target Plasmodium species, the causative agents of malaria, are needed. The enzyme N -myristoyltransferase (NMT) is an essential protein, which catalyzes the myristoylation of protein substrates, often to mediate membrane targeting. We screened ∼1.8 million small molecules for activity against Plasmodium vivax ( P. vivax ) NMT. Hits were triaged based on potency and physicochemical properties and further tested against P. vivax and Plasmodium falciparum ( P. falciparum ) NMTs. We assessed the activity of hits against human NMT1 and NMT2 and discarded compounds with low selectivity indices. We identified 23 chemical classes specific for the inhibition of Plasmodium NMTs over human NMTs, including multiple novel scaffolds. Cocrystallization of P. vivax NMT with one compound revealed peptide binding pocket binding. Other compounds show a range of potential modes of action. Our data provide insight into the activity of a collection of selective inhibitors of Plasmodium NMT and serve as a starting point for subsequent medicinal chemistry efforts.


  • Organizational Affiliation
    • Center for Infectious Disease Research , Seattle , Washington 98109 , United States.

Macromolecule Content 

  • Total Structure Weight: 146.1 kDa 
  • Atom Count: 11,688 
  • Modeled Residue Count: 1,148 
  • Deposited Residue Count: 1,215 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycylpeptide N-tetradecanoyltransferase
A, B, C
405Plasmodium vivax Sal-1Mutation(s): 0 
Gene Names: PVX_085815
EC: 2.3.1.97
UniProt
Find proteins for A5K1A2 (Plasmodium vivax (strain Salvador I))
Explore A5K1A2 
Go to UniProtKB:  A5K1A2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5K1A2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MYA

Query on MYA



Download:Ideal Coordinates CCD File
H [auth A],
M [auth B],
P [auth C]
TETRADECANOYL-COA
C35 H62 N7 O17 P3 S
DUAFKXOFBZQTQE-QSGBVPJFSA-N
L7Y

Query on L7Y



Download:Ideal Coordinates CCD File
G [auth A],
L [auth B]
5-(4-chlorophenyl)-3-({[3-(morpholine-4-carbonyl)phenyl]amino}methyl)pyridin-2(1H)-one
C23 H22 Cl N3 O3
FGOXIGQZSJLIHW-UHFFFAOYSA-N
OXM

Query on OXM



Download:Ideal Coordinates CCD File
F [auth A]OXAMIC ACID
C2 H3 N O3
SOWBFZRMHSNYGE-UHFFFAOYSA-N
BME

Query on BME



Download:Ideal Coordinates CCD File
I [auth A],
O [auth B],
Q [auth C]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
N [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A],
K [auth B],
R [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A],
J [auth B],
S [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.174 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.149 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.150 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.42α = 90
b = 119.03β = 90
c = 175.35γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21AI137815

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-01
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references
  • Version 1.2: 2020-02-05
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description