SMTL ID : 8bt7.1

Notum Inhibitor ARUK3004903

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 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, Q.132, R.136 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.19, A:Q.132 Water bridges: A:E.133

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

SO4.2: 4 residues within 4Å: Chain A: R.332, H.335, R.339, C.355 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.339 Salt bridges: A:R.332, A:H.335, A:R.339 SO4.3: 5 residues within 4Å: Chain A: R.56, K.120, N.121, E.122, Y.220 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.122 Water bridges: A:R.56, A:Y.123 Salt bridges: A:R.56 SO4.4: 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 SO4.13: 2 residues within 4Å: Chain A: K.326, V.360 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.326, A:H.358, A:V.360 Salt bridges: A:K.326 SO4.14: 4 residues within 4Å: Chain A: V.279, Q.280, E.281, R.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.281 Salt bridges: A:R.284

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

DMS.5: 6 residues within 4Å: Chain A: R.42, Y.94, W.95, W.96, N.97, A.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.97, A:A.98 pi-Cation interactions: A:W.96

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

EDO.6: 6 residues within 4Å: Chain A: R.79, T.80, G.81, T.82, L.85, F.102 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.79, A:R.79, A:T.80, A:T.82, A:T.82 EDO.7: 6 residues within 4Å: Chain A: W.190, Y.245, Y.248, P.249, T.297, V.301 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.245 EDO.8: 5 residues within 4Å: Chain A: S.40, R.41, R.42, N.97, K.147 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.41, A:N.97, A:K.147, A:K.147 EDO.9: 4 residues within 4Å: Chain A: L.14, L.16, S.72, W.75 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.72 EDO.10: 2 residues within 4Å: Chain A: P.76, R.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.77 EDO.11: 5 residues within 4Å: Chain A: Y.248, L.251, S.253, P.254, V.255 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.248, A:L.251, A:V.255 Water bridges: A:L.251

1 x RL6: 1-[3,4-bis(chloranyl)-5-methyl-indol-1-yl]ethanone(Non-covalent)

RL6.12: 12 residues within 4Å: Chain A: W.51, Y.52, V.110, A.156, T.159, F.191, P.210, I.214, F.242, F.243, A.265, V.269 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.51, A:W.51, A:F.191, A:F.191, A:P.210, A:A.265, A:V.269, A:V.269 Hydrogen bonds: A:W.51, 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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