Notum Fragment 609

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

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Structural Analysis and Development of Notum Fragment Screening Hits.

Zhao, Y.Mahy, W.Willis, N.J.Woodward, H.L.Steadman, D.Bayle, E.D.Atkinson, B.N.Sipthorp, J.Vecchia, L.Ruza, R.R.Harlos, K.Jeganathan, F.Constantinou, S.Costa, A.Kjaer, S.Bictash, M.Salinas, P.C.Whiting, P.Vincent, J.P.Fish, P.V.Jones, E.Y.

(2022) ACS Chem Neurosci 13: 2060-2077

  • DOI: https://doi.org/10.1021/acschemneuro.2c00325
  • Primary Citation of Related Structures:  
    7B4X, 7B84, 7B86, 7B87, 7B89, 7B8C, 7B8D, 7B8F, 7B8G, 7B8J, 7B8K, 7B8L, 7B8M, 7B8N, 7B8O, 7B8U, 7B8X, 7B8Y, 7B8Z, 7B98, 7B99, 7B9D, 7B9I, 7B9N, 7B9U, 7BA1, 7BAC, 7BAP, 7BC8, 7BC9, 7BCC, 7BCD, 7BCF, 7BCH, 7BCI, 7BCK, 7BCL, 7BD2, 7BD3, 7BD4, 7BD5, 7BD6, 7BD8, 7BD9, 7BDA, 7BDB, 7BDC, 7BDD, 7BDF, 7BDG

  • PubMed Abstract: 

    The Wnt signaling suppressor Notum is a promising target for osteoporosis, Alzheimer's disease, and colorectal cancers. To develop novel Notum inhibitors, we used an X-ray crystallographic fragment screen with the Diamond-SGC Poised Library (DSPL) and identified 59 fragment hits from the analysis of 768 data sets. Fifty-eight of the hits were found bound at the enzyme catalytic pocket with potencies ranging from 0.5 to >1000 μM. Analysis of the fragments' diverse binding modes, enzymatic inhibitory activities, and chemical properties led to the selection of six hits for optimization, and five of these resulted in improved Notum inhibitory potencies. One hit, 1 - phenyl-1,2,3-triazole 7 , and its related cluster members, have shown promising lead-like properties. These became the focus of our fragment development activities, resulting in compound 7d with IC 50 0.0067 μM. The large number of Notum fragment structures and their initial optimization provided an important basis for further Notum inhibitor development.

  • Organizational Affiliation

    Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
O3D (Subject of Investigation/LOI)
Query on O3D

Download Ideal Coordinates CCD File 
K [auth A]4-[(furan-2-yl)methyl]-1lambda~6~,4-thiazinane-1,1-dione
C9 H13 N O3 S
Query on SO4

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

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

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.364α = 90
b = 72.871β = 90
c = 78.873γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC375/A17721

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