SMTL ID : 8bta.1

Notum Inhibitor ARUK3004308

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

monomer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.19, V.22, L.129, R.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.19, A:R.136

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

SO4.2: 3 residues within 4Å: Chain A: R.228, R.231, R.252 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.231, A:R.252 Salt bridges: A:R.228 SO4.10: 4 residues within 4Å: Chain A: T.65, M.66, R.67, R.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.67, A:R.68 Salt bridges: A:R.68 SO4.11: 3 residues within 4Å: Chain A: R.13, H.15, R.141 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.13, A:H.15, A:R.141

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

DMS.3: 5 residues within 4Å: Chain A: R.42, Y.94, W.95, W.96, N.97 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.97, A:A.98 pi-Cation interactions: A:W.96 DMS.7: 5 residues within 4Å: Chain A: R.56, K.120, N.121, E.122, Y.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.56 DMS.8: 6 residues within 4Å: Chain A: Y.33, E.48, R.68, W.75, P.76, R.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.33, A:R.79 Salt bridges: A:E.48 DMS.9: 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

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: R.295, H.296, K.299 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.295, A:H.296, A:K.299 Water bridges: A:R.295 EDO.5: 5 residues within 4Å: Chain A: K.299, D.300, V.301, P.302, H.358 No protein-ligand interaction detected (PLIP)

1 x RC6: 1-(4-chloranyl-2,3-dihydroindol-1-yl)ethanone(Non-covalent)

RC6.6: 11 residues within 4Å: Chain A: W.51, Y.52, V.110, S.155, A.156, T.159, F.191, P.210, I.214, F.243, A.265 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.51, A:V.110, A:T.159, A:F.191, A:I.214, A:A.265 Hydrogen bonds: A:W.51 Water bridges: A:A.156 pi-Stacking: A:Y.52, A:F.191

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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