SMTL ID : 8bsp.1

Notum Inhibitor ARUK3006560

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: T.65, M.66, R.67, R.68 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.67, A:R.68 Water bridges: A:M.66, A:R.68 Salt bridges: A:R.68 SO4.2: 5 residues within 4Å: Chain A: R.56, K.120, N.121, E.122, Y.220 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.120, A:E.122, A:Y.220 Water bridges: A:Y.123, A:Y.123 Salt bridges: A:R.56 SO4.6: 3 residues within 4Å: Chain A: Y.197, R.198, L.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.197 Water bridges: A:Q.280 Salt bridges: A:R.198 SO4.7: 2 residues within 4Å: Chain A: R.228, R.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.231 Salt bridges: A:R.228 SO4.8: 5 residues within 4Å: Chain A: R.167, E.170, V.225, E.227, R.230 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.170, A:V.225, A:E.227 Salt bridges: A:R.167, A:R.230

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 3 residues within 4Å: Chain A: N.19, V.22, R.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.19

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 6 residues within 4Å: Chain A: Y.248, L.251, R.252, S.253, P.254, V.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.248, A:V.255

1 x RD9: methyl 4-oxidanylidene-4-[4-(trifluoromethyl)-2,3-dihydroindol-1-yl]butanoate(Non-covalent)

RD9.5: 10 residues within 4Å: Chain A: W.51, V.110, S.155, A.156, T.159, F.191, P.210, I.214, F.242, F.243 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.51, A:V.110, A:F.191, A:F.191 Hydrogen bonds: A:W.51 pi-Stacking: A:Y.52, A:F.191 Halogen bonds: A:F.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Atkinson, B.N. et al., Designed switch from covalent to non-covalent inhibitors of carboxylesterase Notum activity. Eur.J.Med.Chem. (2023)

Release Date

2022-12-14

Peptides

Palmitoleoyl-protein carboxylesterase NOTUM: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Palmitoleoyl-protein carboxylesterase NOTUM

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