6ZUV

Notum fragment 286


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

5-Phenyl-1,3,4-oxadiazol-2(3 H )-ones Are Potent Inhibitors of Notum Carboxylesterase Activity Identified by the Optimization of a Crystallographic Fragment Screening Hit.

Mahy, W.Willis, N.J.Zhao, Y.Woodward, H.L.Svensson, F.Sipthorp, J.Vecchia, L.Ruza, R.R.Hillier, J.Kjaer, S.Frew, S.Monaghan, A.Bictash, M.Salinas, P.C.Whiting, P.Vincent, J.P.Jones, E.Y.Fish, P.V.

(2020) J Med Chem 63: 12942-12956

  • DOI: 10.1021/acs.jmedchem.0c01391
  • Primary Citation of Related Structures:  
    6ZVL, 6ZUV

  • PubMed Abstract: 
  • Carboxylesterase Notum is a negative regulator of the Wnt signaling pathway. There is an emerging understanding of the role Notum plays in disease, supporting the need to discover new small-molecule inhibitors. A crystallographic X-ray fragment screen was performed, which identified fragment hit 1,2,3-triazole 7 as an attractive starting point for a structure-based drug design hit-to-lead program ...

    Carboxylesterase Notum is a negative regulator of the Wnt signaling pathway. There is an emerging understanding of the role Notum plays in disease, supporting the need to discover new small-molecule inhibitors. A crystallographic X-ray fragment screen was performed, which identified fragment hit 1,2,3-triazole 7 as an attractive starting point for a structure-based drug design hit-to-lead program. Optimization of 7 identified oxadiazol-2-one 23dd as a preferred example with properties consistent with drug-like chemical space. Screening 23dd in a cell-based TCF/LEF reporter gene assay restored the activation of Wnt signaling in the presence of Notum. Mouse pharmacokinetic studies with oral administration of 23dd demonstrated good plasma exposure and partial blood-brain barrier penetration. Significant progress was made in developing fragment hit 7 into lead 23dd (>600-fold increase in activity), making it suitable as a new chemical tool for exploring the role of Notum-mediated regulation of Wnt signaling.


    Organizational Affiliation

    The Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Palmitoleoyl-protein carboxylesterase NOTUMA383Homo sapiensMutation(s): 1 
Gene Names: NOTUMOK/SW-CL.30
EC: 3.1.1.98
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P988 (Homo sapiens)
Explore Q6P988 
Go to UniProtKB:  Q6P988
PHAROS:  Q6P988
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.673α = 90
b = 72.284β = 90
c = 79.001γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-07-23 
  • Released Date: 2020-11-11 
  • Deposition Author(s): Zhao, Y., Jones, E.Y.

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

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references