SMTL ID : 8bti.1

Notum Inhibitor ARUK3004556

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.31 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, Q.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.19, A:Q.132

5 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.120, A:E.122, A:Y.220, A:Y.220 Water bridges: A:Y.123, A:Y.123 Salt bridges: A:R.56 SO4.3: 6 residues within 4Å: Chain A: R.167, E.170, V.225, E.227, R.230 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.227 Salt bridges: A:R.167, A:R.230 SO4.4: 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 SO4.15: 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 SO4.16: 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

1 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

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

EDO.6: 3 residues within 4Å: Chain A: R.295, H.296, K.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.296, A:K.299 EDO.7: 6 residues within 4Å: Chain A: Y.248, L.251, R.252, S.253, P.254, V.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.248, A:V.255, A:V.255 EDO.8: 5 residues within 4Å: Chain A: D.166, R.167, P.226, E.227 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.167, A:E.227 EDO.9: 5 residues within 4Å: Chain A: K.299, D.300, V.301, P.302, H.358 No protein-ligand interaction detected (PLIP) EDO.11: 6 residues within 4Å: Chain A: W.260, I.315, R.317, W.320, V.323, L.330 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.317, A:R.317, A:W.320 Water bridges: A:W.260, A:E.313, A:V.323 EDO.12: 7 residues within 4Å: Chain A: E.264, L.310, S.311, H.312, E.313, P.373, G.375 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.312, A:H.312, A:E.313, A:P.373 EDO.13: 4 residues within 4Å: Chain A: G.39, S.40, R.41, R.42 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.41 EDO.14: 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

1 x RFO: 1-(4-chloranylindol-1-yl)-2-methoxy-ethanone(Non-covalent)

RFO.10: 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 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.110, A:F.191, A:F.191, A:I.214 Hydrogen bonds: A:W.51, A:A.156 Water bridges: A:S.155 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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