SMTL ID : 8bsr.1

Notum Inhibitor ARUK3006562

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

6 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:L.69 Salt bridges: A:R.68 SO4.2: 5 residues within 4Å: Chain A: R.56, K.120, N.121, E.122, Y.220 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.120, A:E.122, A:Y.220 Water bridges: A:Y.123 Salt bridges: A:R.56 SO4.9: 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:P.278 Salt bridges: A:R.198 SO4.10: 1 residues within 4Å: Chain A: R.228 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.228 SO4.11: 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 SO4.12: 3 residues within 4Å: Chain A: R.317, S.318, H.319 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.318, A:H.319 Salt bridges: A:R.317, A:H.319

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 RCU: ethyl 4-[5-chloranyl-4-(trifluoromethyl)-2,3-dihydroindol-1-yl]-4-oxidanylidene-butanoate(Non-covalent)

RCU.5: 14 residues within 4Å: Chain A: G.50, W.51, Y.52, S.155, A.156, T.159, F.191, P.210, I.214, F.242, F.243, A.265, V.269, H.312 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.51, A:A.156, A:F.191, A:V.269 pi-Stacking: A:F.191 Halogen bonds: A:T.159

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

EDO.6: 5 residues within 4Å: Chain A: R.42, Y.94, W.95, W.96, N.97 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.42, A:W.95, A:N.97, A:A.98 EDO.7: 3 residues within 4Å: Chain A: S.40, R.41, R.42 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.41 EDO.8: 6 residues within 4Å: Chain A: R.79, T.80, G.81, T.82, L.85, F.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.79, A:R.79, A:T.82, A:T.82

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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