SMTL ID : 8bte.1

Notum Inhibitor ARUK3004470

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.19

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

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 SO4.3: 2 residues within 4Å: Chain A: R.228, R.231 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.231, A:R.252 Salt bridges: A:R.228 SO4.9: 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 SO4.10: 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 SO4.11: 1 residues within 4Å: Chain A: R.68 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.68 SO4.12: 3 residues within 4Å: Chain A: Y.197, R.198, L.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.197 Salt bridges: A:R.198

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

DMS.4: 5 residues within 4Å: Chain A: R.42, Y.94, W.95, W.96, N.97 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.97 pi-Cation interactions: A:W.96

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

EDO.5: 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.6: 5 residues within 4Å: Chain A: K.299, D.300, V.301, P.302, H.358 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.300 EDO.7: 4 residues within 4Å: Chain A: P.351, P.356, V.357, H.358 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.358 Water bridges: A:L.352, A:L.352

1 x RIX: methyl 2-(4-chloranylindol-1-yl)-2-oxidanylidene-ethanoate(Non-covalent)

RIX.8: 12 residues within 4Å: Chain A: W.51, Y.52, S.155, A.156, T.159, F.191, P.210, I.214, F.242, F.243, A.265, H.312 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.159, A:F.191, A:I.214, A:F.243 Hydrogen bonds: A:W.51, A:A.156, A:T.159 pi-Stacking: A:Y.52, A:F.191, 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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