6R8R

Structure of the Wnt deacylase Notum in complex with isoquinoline 45


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Discovery of 2-phenoxyacetamides as inhibitors of the Wnt-depalmitoleating enzyme NOTUM from an X-ray fragment screen.

Atkinson, B.N.Steadman, D.Zhao, Y.Sipthorp, J.Vecchia, L.Ruza, R.R.Jeganathan, F.Lines, G.Frew, S.Monaghan, A.Kjær, S.Bictash, M.Jones, E.Y.Fish, P.V.

(2019) Medchemcomm 10: 1361-1369

  • DOI: 10.1039/c9md00096h
  • Primary Citation of Related Structures:  
    6R8Q, 6R8P, 6R8R

  • PubMed Abstract: 
  • NOTUM is a carboxylesterase that has been shown to act by mediating the O -depalmitoleoylation of Wnt proteins resulting in suppression of Wnt signaling. Here, we describe the development of NOTUM inhibitors that restore Wnt signaling for use in ...

    NOTUM is a carboxylesterase that has been shown to act by mediating the O -depalmitoleoylation of Wnt proteins resulting in suppression of Wnt signaling. Here, we describe the development of NOTUM inhibitors that restore Wnt signaling for use in in vitro disease models where NOTUM over activity is an underlying cause. A crystallographic fragment screen with NOTUM identified 2-phenoxyacetamide 3 as binding in the palmitoleate pocket with modest inhibition activity (IC 50 33 μM). Optimization of hit 3 by SAR studies guided by SBDD identified indazole 38 (IC 50 0.032 μM) and isoquinoline 45 (IC 50 0.085 μM) as potent inhibitors of NOTUM. The binding of 45 to NOTUM was rationalized through an X-ray co-crystal structure determination which showed a flipped binding orientation compared to 3 . However, it was not possible to combine NOTUM inhibition activity with metabolic stability as the majority of the compounds tested were rapidly metabolized in an NADPH-independent manner.


    Organizational Affiliation

    The Francis Crick Institute , 1 Midland Road , London , NW1 1AT , UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Palmitoleoyl-protein carboxylesterase NOTUM A383Homo sapiensMutation(s): 1 
Gene Names: NOTUMOK/SW-CL.30
EC: 3.1.1.98
Find proteins for Q6P988 (Homo sapiens)
Explore Q6P988 
Go to UniProtKB:  Q6P988
NIH Common Fund Data Resources
PHAROS:  Q6P988
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JV8
Query on JV8

Download Ideal Coordinates CCD File 
A
~{N}-isoquinolin-6-yl-2-(2-methylphenoxy)ethanamide
C18 H16 N2 O2
PEVCERQGPZRIFE-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JV8IC50:  85   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.34α = 90
b = 71.72β = 90
c = 78.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC375/A17721
Medical Research Council (United Kingdom)United KingdomMR/M000141/1

Revision History 

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection
  • Version 1.2: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary