6R8P

Notum fragment 723

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

  • Deposited: 2019-04-02 Released: 2019-05-08 
  • 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: 1.45 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Discovery of 2-phenoxyacetamides as inhibitors of the Wnt-depalmitoleating enzyme NOTUM from an X-ray fragment screen.

Atkinson, B.N., Steadman, D., Zhao, Y., Sipthorp, J., Vecchia, L., Ruza, R.R., Jeganathan, F., Lines, G., Frew, S., Monaghan, A., Kjær, S., Bictash, M., Jones, E.Y., Fish, P.V.

(2019) Medchemcomm 10: 1361-1369

  • DOI: 10.1039/c9md00096h
  • Primary Citation of Related Structures:  
    6R8Q, 6R8P, 6R8R

  • PubMed Abstract: 

    • NOTUM is a carboxylesterase that has been shown to act by mediating the O -depalmitoleoylation of Wnt proteins resulting in suppression of Wnt signaling. Here, we describe the development of NOTUM inhibitors that restore Wnt signaling for use in ...

    NOTUM is a carboxylesterase that has been shown to act by mediating the O -depalmitoleoylation of Wnt proteins resulting in suppression of Wnt signaling. Here, we describe the development of NOTUM inhibitors that restore Wnt signaling for use in in vitro disease models where NOTUM over activity is an underlying cause. A crystallographic fragment screen with NOTUM identified 2-phenoxyacetamide 3 as binding in the palmitoleate pocket with modest inhibition activity (IC 50 33 μM). Optimization of hit 3 by SAR studies guided by SBDD identified indazole 38 (IC 50 0.032 μM) and isoquinoline 45 (IC 50 0.085 μM) as potent inhibitors of NOTUM. The binding of 45 to NOTUM was rationalized through an X-ray co-crystal structure determination which showed a flipped binding orientation compared to 3 . However, it was not possible to combine NOTUM inhibition activity with metabolic stability as the majority of the compounds tested were rapidly metabolized in an NADPH-independent manner.

    Organizational Affiliation: 

    The Francis Crick Institute , 1 Midland Road , London , NW1 1AT , 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: NOTUM, OK/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
GTEx:  ENSG00000185269
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JVB
Query on JVB
Download Ideal Coordinates CCD File 
A
2-(2-methylphenoxy)-~{N}-pyridin-3-yl-ethanamide
C14 H14 N2 O2
MUOTYWWZYLNCGX-UHFFFAOYSA-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
GOL
Query on GOL
Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JVBIC50:  33000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.615α = 90
b = 72.791β = 90
c = 78.867γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-04-02 
  • Released Date: 2019-05-08 
    • 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: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection
  • Version 1.2: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Refinement description, Structure summary