5O48 | pdb_00005o48

P.vivax NMT with an aminomethylindazole inhibitor bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 
    0.200 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NHWClick on this verticalbar to view detailsBest fitted 9K2Click on this verticalbar to view details

This is version 1.3 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: https://doi.org/10.1038/s41557-018-0039-2
  • Primary Citation of Related Structures:  
    5MU6, 5O48, 5O4V, 5O6H, 5O6J

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycylpeptide N-tetradecanoyltransferase
A, B, C
385Plasmodium vivaxMutation(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
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NHW
Query on NHW

Download Ideal Coordinates CCD File 
D [auth A],
N [auth B],
U [auth C]
2-oxopentadecyl-CoA
C36 H64 N7 O17 P3 S
JKWHUJMJVNMKEF-UOCZADIYSA-J
9K2
Query on 9K2

Download Ideal Coordinates CCD File 
E [auth A],
O [auth B],
V [auth C]
1-[5-(4-fluoranyl-2-methyl-phenyl)-1~{H}-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine
C17 H18 F N3
DBUAKDPVYBEAFM-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C],
K [auth A],
L [auth A],
M [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS
Query on DMS

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
P [auth B]
Q [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth A],
T [auth B],
Z [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A],
S [auth B],
Y [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.565α = 90
b = 121.983β = 90
c = 178.247γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NHWClick on this verticalbar to view detailsBest fitted 9K2Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom087792

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-05-23
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-04
    Changes: Data collection, Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations