6T2H

Furano[2,3-d]prymidine amides as Notum inhibitors

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2019-10-08 Released: 2020-01-01 
  • Deposition Author(s): Zhao, Y., Jones, E.Y.
  • Funding Organization(s): Medical Research Council (United Kingdom), Cancer Research UK

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Scaffold-hopping identifies furano[2,3-d]pyrimidine amides as potent Notum inhibitors.

Atkinson, B.N.Steadman, D.Mahy, W.Zhao, Y.Sipthorp, J.Bayle, E.D.Svensson, F.Papageorgiou, G.Jeganathan, F.Frew, S.Monaghan, A.Bictash, M.Jones, E.Y.Fish, P.V.

(2020) Bioorg Med Chem Lett 30: 126751-126751

  • DOI: 10.1016/j.bmcl.2019.126751
  • Primary Citation of Related Structures:  
    6T2H, 6T2K

  • PubMed Abstract: 
  • The carboxylesterase Notum is a key negative regulator of the Wnt signaling pathway by mediating the depalmitoleoylation of Wnt proteins. Our objective was to discover potent small molecule inhibitors of Notum suitable for exploring the regulation of Wnt ...

    The carboxylesterase Notum is a key negative regulator of the Wnt signaling pathway by mediating the depalmitoleoylation of Wnt proteins. Our objective was to discover potent small molecule inhibitors of Notum suitable for exploring the regulation of Wnt signaling in the central nervous system. Scaffold-hopping from thienopyrimidine acids 1 and 2, supported by X-ray structure determination, identified 3-methylimidazolin-4-one amides 20-24 as potent inhibitors of Notum with activity across three orthogonal assay formats (biochemical, extra-cellular, occupancy). A preferred example 24 demonstrated good stability in mouse microsomes and plasma, and cell permeability in the MDCK-MDR1 assay albeit with modest P-gp mediated efflux. Pharmacokinetic studies with 24 were performed in vivo in mouse with single oral administration of 24 showing good plasma exposure and reasonable CNS penetration. We propose that 24 is a new chemical tool suitable for cellular studies to explore the fundamental biology of Notum.


    Organizational Affiliation

    Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, UK; The Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, UK. Electronic address: p.fish@ucl.ac.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
M9N
Query on M9N

Download Ideal Coordinates CCD File 
A
2-[[(4~{S})-5-chloranyl-6-methyl-1,2,3,4-tetrahydrothieno[2,3-d]pyrimidin-4-yl]sulfanyl]ethanoic acid
C9 H11 Cl N2 O2 S2
YXTHLXJCVDULSY-QMMMGPOBSA-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.72α = 90
b = 71.89β = 90
c = 78.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PDB_EXTRACTdata extraction
DIALSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-10-08 
  • Released Date: 2020-01-01 
  • Deposition Author(s): Zhao, Y., Jones, E.Y.

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

Revision History 

  • Version 1.0: 2020-01-01
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary