6T2H

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

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

  • 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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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 ...

    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.,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.,Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, UK.,The Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Palmitoleoyl-protein carboxylesterase NOTUM
A
383Homo sapiensMutation(s): 1 
Gene Names: NOTUM
EC: 3.1.1.98
Find proteins for Q6P988 (Homo sapiens)
Go to Gene View: NOTUM
Go to UniProtKB:  Q6P988
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
M9N
Query on M9N

Download SDF File 
Download 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.720α = 90.00
b = 71.890β = 90.00
c = 78.130γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references