SMTL ID : 6tr7.1

N-[2-(5-fluoro-1H-indol-3-yl)ethyl]acetamide-Notum complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.295, K.326, V.360 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.295, A:K.326, A:H.358, A:V.360 Salt bridges: A:R.295, A:K.326 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:E.122, A:Y.220 Water bridges: A:R.56, A:Y.123, A:Y.123 Salt bridges: A:R.56 SO4.3: 6 residues within 4Å: Chain A: R.42, Y.94, W.95, W.96, N.97, A.98 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.93, A:W.96, A:N.97, A:A.98 Salt bridges: A:R.42 SO4.4: 3 residues within 4Å: Chain A: P.356, V.357, H.358 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.356, A:V.357, A:H.358 SO4.5: 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 SO4.6: 4 residues within 4Å: Chain A: T.65, M.66, R.67, R.68 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.67, A:R.68 Water bridges: A:D.74 Salt bridges: A:R.68

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

EDO.7: 7 residues within 4Å: Chain A: G.50, W.51, S.155, A.156, F.191, A.265 Ligands: HWH.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.50, A:W.51, A:A.156 EDO.8: 3 residues within 4Å: Chain A: L.175, G.176, Y.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.176 EDO.9: 4 residues within 4Å: Chain A: R.13, K.35, E.36, R.38 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.13, A:R.13, A:E.36, A:R.38 EDO.10: 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:L.251, A:V.255, A:V.255 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:D.187, A:W.260, A:V.323 EDO.12: 3 residues within 4Å: Chain A: R.317, P.373, T.374 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.374 Water bridges: A:H.319 EDO.13: 2 residues within 4Å: Chain A: R.339, H.342 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.339 EDO.14: 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:R.295, A:K.299 Water bridges: A:H.296 EDO.15: 5 residues within 4Å: Chain A: Y.33, W.75, P.76, R.79, P.104 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.79 Water bridges: A:R.68 EDO.16: 7 residues within 4Å: Chain A: R.79, T.80, G.81, T.82, L.85, F.102, I.316 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.79, A:R.79, A:T.82, A:T.82 Water bridges: A:T.80 EDO.17: 6 residues within 4Å: Chain A: Q.324, V.325, K.326, G.327, N.369, P.370 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.327 Water bridges: A:K.326, A:K.326 EDO.18: 2 residues within 4Å: Chain A: P.76, R.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.77

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.19: 2 residues within 4Å: Chain A: N.19, V.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.19 Water bridges: A:E.133

2 x HWH: ~{N}-[2-(5-fluoranyl-1~{H}-indol-3-yl)ethyl]ethanamide(Non-covalent)

HWH.20: 12 residues within 4Å: Chain A: W.51, Y.52, V.110, A.156, T.159, F.191, P.210, F.242, F.243, A.265, V.269 Ligands: EDO.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.51, A:Y.52, A:V.110, A:A.156, A:F.191, A:P.210, A:F.243, A:V.269 Hydrogen bonds: A:T.159 pi-Stacking: A:F.191, A:F.191 HWH.21: 6 residues within 4Å: Chain A: L.192, D.193, N.194, K.195, P.210, T.211 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.210 Hydrogen bonds: A:N.194, A:T.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Structural characterization of melatonin as an inhibitor of the Wnt deacylase Notum. J. Pineal Res. (2020)

Release Date

2020-01-08

Peptides

Palmitoleoyl-protein carboxylesterase NOTUM: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Palmitoleoyl-protein carboxylesterase NOTUM

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