6MB1

Crystal structure of N-myristoyl transferase (NMT) from Plasmodium vivax in complex with inhibitor IMP-1002


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-Guided Identification of Resistance Breaking Antimalarial N‐Myristoyltransferase Inhibitors.

Schlott, A.C.Mayclin, S.Reers, A.R.Coburn-Flynn, O.Bell, A.S.Green, J.Knuepfer, E.Charter, D.Bonnert, R.Campo, B.Burrows, J.Lyons-Abbott, S.Staker, B.L.Chung, C.W.Myler, P.J.Fidock, D.A.Tate, E.W.Holder, A.A.

(2019) Cell Chem Biol 26: 991

  • DOI: 10.1016/j.chembiol.2019.03.015
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The attachment of myristate to the N-terminal glycine of certain proteins is largely a co-translational modification catalyzed by N-myristoyltransferase (NMT), and involved in protein membrane-localization. Pathogen NMT is a validated therapeutic tar ...

    The attachment of myristate to the N-terminal glycine of certain proteins is largely a co-translational modification catalyzed by N-myristoyltransferase (NMT), and involved in protein membrane-localization. Pathogen NMT is a validated therapeutic target in numerous infectious diseases including malaria. In Plasmodium falciparum, NMT substrates are important in essential processes including parasite gliding motility and host cell invasion. Here, we generated parasites resistant to a particular NMT inhibitor series and show that resistance in an in vitro parasite growth assay is mediated by a single amino acid substitution in the NMT substrate-binding pocket. The basis of resistance was validated and analyzed with a structure-guided approach using crystallography, in combination with enzyme activity, stability, and surface plasmon resonance assays, allowing identification of another inhibitor series unaffected by this substitution. We suggest that resistance studies incorporated early in the drug development process help selection of drug combinations to impede rapid evolution of parasite resistance.


    Organizational Affiliation

    Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA; Department of Biomedical Informatics & Medical Education, University of Washington, Seattle, USA; Department of Global Health, University of Washington, Seattle, USA.,Molecular Sciences Research Hub, Imperial College, White City Campus Wood Lane, London W12 0BZ, UK. Electronic address: e.tate@imperial.ac.uk.,Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA.,Structural and Biophysical Sciences, GlaxoSmithKline, Stevenage, Hertfordshire, UK.,Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, 1215 Geneva 15, Switzerland.,Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA.,Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Molecular Sciences Research Hub, Imperial College, White City Campus Wood Lane, London W12 0BZ, UK. Electronic address: anja.schlott@crick.ac.uk.,Molecular Sciences Research Hub, Imperial College, White City Campus Wood Lane, London W12 0BZ, UK.,Structural and Biophysical Sciences, GlaxoSmithKline, Stevenage, Hertfordshire, UK; Crick-GSK Biomedical LinkLabs, GSK Medicines Research Centre, Stevenage, UK.,Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA.,Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK. Electronic address: tony.holder@crick.ac.uk.,Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA.,Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycylpeptide N-tetradecanoyltransferase
A, B, C
405Plasmodium vivaxMutation(s): 0 
EC: 2.3.1.97
Find proteins for A0A1G4HIY1 (Plasmodium vivax)
Go to UniProtKB:  A0A1G4HIY1
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JCY
Query on JCY

Download SDF File 
Download CCD File 
A, B, C
1-(5-{4-fluoro-2-[2-(1,3,5-trimethyl-1H-pyrazol-4-yl)ethoxy]phenyl}-1-methyl-1H-indazol-3-yl)-N,N-dimethylmethanamine
C25 H30 F N5 O
YEOAAQMCKFJWKF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
YNC
Query on YNC

Download SDF File 
Download CCD File 
A, B, C
TETRADEC-13-YNOIC ACID - COA THIOESTER
C35 H58 N7 O17 P3 S
YPDKCQHYDROOAS-QSGBVPJFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 57.560α = 90.00
b = 119.110β = 90.00
c = 176.080γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHENIXphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-07-31
    Type: Data collection, Database references