› 6r8q

X-ray diffraction
1.5Å resolution

STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH A BENZOTRIAZOLE FRAGMENT

Released:
DOI: 10.2210/pdb6r8q/pdb
PDB entry 6r8q coloured by chain, front view.
PDB entry 6r8q coloured by chain, side view.
PDB entry 6r8q coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of 2-phenoxyacetamides as inhibitors of the Wnt-depalmitoleating enzyme NOTUM from an X-ray fragment screen.
Atkinson BN, Steadman D, Zhao Y, Sipthorp J, Vecchia L, Ruza RR, Jeganathan F, Lines G, Frew S, Monaghan A, Kjær S, Bictash M, Jones EY, Fish PV
OpenAccess logo Medchemcomm 10 1361-1369 (2019)
PMID: 31534655

Function and Biology Details

Reaction catalysed: 
[Wnt]-O-(9Z)-hexadec-9-enoyl-L-serine + H(2)O = [Wnt]-L-serine + (9Z)-hexadec-9-enoate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180133 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Palmitoleoyl-protein carboxylesterase NOTUM Chain: A
Molecule details ›
Chain: A
Length: 383 amino acids
Theoretical weight: 43.57 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q6P988 (Residues: 81-451; Coverage: 78%)
Gene names: NOTUM, OK/SW-CL.30
Sequence domains: Pectinacetylesterase

Ligands and Environments

4 bound ligands:
Ligand NAG 1 x NAG
Ligand SO4 8 x SO4
Ligand EDO 5 x EDO
Ligand JV5 1 x JV5
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P212121
Unit cell:
a: 60.099Å b: 71.262Å c: 78.255Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.157 0.155 0.195
Expression system: Homo sapiens

Quick links

Citations

2 review citations

Wnt signaling activation: targets and therapeutic opportunities for stem cell therapy and regenerative medicine.
Bonnet et al. (2021)
1 more

4 mentions without citation

Carboxylesterase Notum Is a Druggable Target to Modulate Wnt Signaling.
Bayle et al. (2021)
3 more