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 6ZUV | pdb_00006zuv

Notum fragment 286


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 
    0.259 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6ZUV

Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acs.jmedchem.0c01391
  • Primary Citation Related Structures: 
    6ZUV, 6ZVL

  • 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. 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: 
    • Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.

Macromolecule Content 

  • Total Structure Weight: 44.76 kDa 
  • Atom Count: 3,074 
  • Modeled Residue Count: 355 
  • Deposited Residue Count: 383 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Palmitoleoyl-protein carboxylesterase NOTUM383Homo sapiensMutation(s): 1 
Gene Names: NOTUM, OK/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
GTEx:  ENSG00000185269 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P988
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q6P988-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
B1J
(Subject of Investigation/LOI)

Query on B1J



Download:Ideal Coordinates CCD File
L [auth A][1-(4-chlorophenyl)-1,2,3-triazol-4-yl]methanol
C9 H8 Cl N3 O
CAHIFLPAMJOAGI-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
K [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
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



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


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
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary