Notum complex with ARUK3003778

Experimental Data Snapshot

  • Resolution: 1.33 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Virtual Screening Directly Identifies New Fragment-Sized Inhibitors of Carboxylesterase Notum with Nanomolar Activity.

Steadman, D.Atkinson, B.N.Zhao, Y.Willis, N.J.Frew, S.Monaghan, A.Patel, C.Armstrong, E.Costelloe, K.Magno, L.Bictash, M.Jones, E.Y.Fish, P.V.Svensson, F.

(2022) J Med Chem 65: 562-578

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01735
  • Primary Citation of Related Structures:  
    7B3G, 7B3H, 7B3I, 7B3P, 7B3X, 7B45, 7B50

  • PubMed Abstract: 

    Notum is a negative regulator of Wnt signaling acting through the hydrolysis of a palmitoleoylate ester, which is required for Wnt activity. Inhibitors of Notum could be of use in diseases where dysfunctional Notum activity is an underlying cause. A docking-based virtual screen (VS) of a large commercial library was used to shortlist 952 compounds for experimental validation as inhibitors of Notum. The VS was successful with 31 compounds having an IC 50 < 500 nM. A critical selection process was then applied with two clusters and two singletons ( 1 - 4d ) selected for hit validation. Optimization of 4d guided by structural biology identified potent inhibitors of Notum activity that restored Wnt/β-catenin signaling in cell-based models. The [1,2,4]triazolo[4,3- b ]pyradizin-3(2 H )-one series 4 represent a new chemical class of Notum inhibitors and the first to be discovered by a VS campaign. These results demonstrate the value of VS with well-designed docking models based on X-ray structures.

  • Organizational Affiliation

    Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, LondonWC1E 6BT, U.K.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Palmitoleoyl-protein carboxylesterase NOTUM383Homo sapiensMutation(s): 1 
Gene Names: NOTUMOK/SW-CL.30
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P988 (Homo sapiens)
Explore Q6P988 
Go to UniProtKB:  Q6P988
GTEx:  ENSG00000185269 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P988
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SXQ (Subject of Investigation/LOI)
Query on SXQ

Download Ideal Coordinates CCD File 
E [auth A]3-(3,4-dichlorophenyl)sulfanyl-1$l^{4},2,7,8-tetrazabicyclo[4.3.0]nona-1(6),2,4,7-tetraen-9-one
C11 H6 Cl2 N4 O S
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
H [auth A],
I [auth A],
J [auth A]
O4 S
Query on DMS

Download Ideal Coordinates CCD File 
D [auth A],
F [auth A],
G [auth A]
C2 H6 O S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.33 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.34α = 90
b = 72.874β = 90
c = 77.901γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-07-27
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description