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: 1.50 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.chembiol.2019.03.015
  • Primary Citation of Related Structures:  
    6MAY, 6MAZ, 6MB0, 6MB1

  • 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 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

    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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycylpeptide N-tetradecanoyltransferase
A, B, C
405Plasmodium vivaxMutation(s): 0 
Gene Names: PVC01_130042700PVP01_1336100
EC: 2.3.1.97
UniProt
Find proteins for A0A1G4HIY1 (Plasmodium vivax)
Explore A0A1G4HIY1 
Go to UniProtKB:  A0A1G4HIY1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1G4HIY1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YNC
Query on YNC

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B],
P [auth C]
TETRADEC-13-YNOIC ACID - COA THIOESTER
C35 H58 N7 O17 P3 S
YPDKCQHYDROOAS-QSGBVPJFSA-N
JCY (Subject of Investigation/LOI)
Query on JCY

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
Q [auth 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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
M [auth B]
N [auth B]
O [auth B]
G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
U [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
R [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.56α = 90
b = 119.11β = 90
c = 176.08γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references