SMTL ID : 8bt8.1

Notum Inhibitor ARUK3004048

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.28 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

7 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 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 SO4.3: 5 residues within 4Å: Chain A: R.167, E.170, V.225, E.227, R.230 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.167, A:R.230 SO4.4: 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 SO4.12: 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 SO4.13: 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 SO4.14: 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 SO4.15: 2 residues within 4Å: Chain A: R.339, H.342 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.339, A:H.342

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

DMS.5: 5 residues within 4Å: Chain A: 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 DMS.11: 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

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

EDO.6: 3 residues within 4Å: Chain A: R.295, H.296, K.299 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.296, A:K.299 Water bridges: A:R.295 EDO.7: 8 residues within 4Å: Chain A: L.192, D.193, N.194, A.209, P.210, T.211, F.243, D.270 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.194, A:N.194, A:T.211, A:T.211 EDO.8: 5 residues within 4Å: Chain A: K.299, D.300, V.301, P.302, H.358 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain A: P.351, P.356, V.357, H.358 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.352, A:H.358

1 x RRI: 1-indol-1-ylethanone(Non-covalent)

RRI.10: 10 residues within 4Å: Chain A: W.51, Y.52, S.155, A.156, T.159, F.191, P.210, I.214, F.242, A.265 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.51, A:Y.52, A:T.159, A:P.210, A:I.214, A:A.265 Water bridges: A:W.51 pi-Stacking: 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

2022-12-28

Peptides

Palmitoleoyl-protein carboxylesterase NOTUM: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Palmitoleoyl-protein carboxylesterase NOTUM

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