5MU6

Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and IMP-1088 inhibitor bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Fragment-derived inhibitors of human N-myristoyltransferase block capsid assembly and replication of the common cold virus.

Mousnier, A.Bell, A.S.Swieboda, D.P.Morales-Sanfrutos, J.Perez-Dorado, I.Brannigan, J.A.Newman, J.Ritzefeld, M.Hutton, J.A.Guedan, A.Asfor, A.S.Robinson, S.W.Hopkins-Navratilova, I.Wilkinson, A.J.Johnston, S.L.Leatherbarrow, R.J.Tuthill, T.J.Solari, R.Tate, E.W.

(2018) Nat Chem 10: 599-606

  • DOI: 10.1038/s41557-018-0039-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Rhinoviruses (RVs) are the pathogens most often responsible for the common cold, and are a frequent cause of exacerbations in asthma, chronic obstructive pulmonary disease and cystic fibrosis. Here we report the discovery of IMP-1088, a picomolar dua ...

    Rhinoviruses (RVs) are the pathogens most often responsible for the common cold, and are a frequent cause of exacerbations in asthma, chronic obstructive pulmonary disease and cystic fibrosis. Here we report the discovery of IMP-1088, a picomolar dual inhibitor of the human N-myristoyltransferases NMT1 and NMT2, and use it to demonstrate that pharmacological inhibition of host-cell N-myristoylation rapidly and completely prevents rhinoviral replication without inducing cytotoxicity. The identification of cooperative binding between weak-binding fragments led to rapid inhibitor optimization through fragment reconstruction, structure-guided fragment linking and conformational control over linker geometry. We show that inhibition of the co-translational myristoylation of a specific virus-encoded protein (VP0) by IMP-1088 potently blocks a key step in viral capsid assembly, to deliver a low nanomolar antiviral activity against multiple RV strains, poliovirus and foot and-mouth disease virus, and protection of cells against virus-induced killing, highlighting the potential of host myristoylation as a drug target in picornaviral infections.


    Organizational Affiliation

    National Heart & Lung Institute, Imperial College London, London, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycylpeptide N-tetradecanoyltransferase 1
A, B
391Homo sapiensMutation(s): 0 
Gene Names: NMT1 (NMT)
EC: 2.3.1.97
Find proteins for P30419 (Homo sapiens)
Go to Gene View: NMT1
Go to UniProtKB:  P30419
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYA
Query on MYA

Download SDF File 
Download CCD File 
A, B
TETRADECANOYL-COA
MYRISTOYL-COA
C35 H62 N7 O17 P3 S
DUAFKXOFBZQTQE-GLTUGWJXDB
 Ligand Interaction
KFK
Query on KFK

Download SDF File 
Download CCD File 
A, B
1-[5-[3,4-bis(fluoranyl)-2-[2-(1,3,5-trimethylpyrazol-4-yl)ethoxy]phenyl]-1-methyl-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine
C25 H29 F2 N5 O
SOXNKJCQBRQUMS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.730α = 90.00
b = 180.730β = 90.00
c = 58.990γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United Kingdom--

Revision History 

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-05-23
    Type: Data collection, Database references
  • Version 1.2: 2018-07-04
    Type: Data collection, Database references