SMTL ID : 6t2k.1

Furano[2,3-d]prymidine amides as Notum inhibitors

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

monomer

Ligands

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

SO4.1: 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 SO4.4: 3 residues within 4Å: Chain A: R.295, K.326, V.360 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.295, A:K.326, A:V.360 Salt bridges: A:R.295, A:K.326 SO4.5: 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:E.122 Water bridges: A:K.120, A:Y.123, A:Y.123 Salt bridges: A:R.56 SO4.6: 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 SO4.7: 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 NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 3 residues within 4Å: Chain A: N.19, V.22, R.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.19 Water bridges: A:E.133

1 x M9K: 2-(6-chloranyl-7-cyclopropyl-thieno[3,2-d]pyrimidin-4-yl)sulfanylethanoic acid(Non-covalent)

M9K.3: 13 residues within 4Å: Chain A: G.50, W.51, S.155, A.156, T.159, F.191, P.210, I.214, F.242, F.243, A.265, V.269, H.312 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.191, A:F.191, A:P.210, A:I.214, A:F.243, A:F.243 Hydrogen bonds: A:G.50, A:W.51, A:S.155, A:A.156 Salt bridges: A:H.312 pi-Stacking: A:F.191, A:F.191

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

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: 3 residues within 4Å: Chain A: R.13, K.35, E.36 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.13, A:R.13, A:E.36, A:E.36 EDO.10: 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 EDO.11: 4 residues within 4Å: Chain A: G.39, S.40, R.41, R.42 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.41, A:R.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Atkinson, B.N. et al., Scaffold-hopping identifies furano[2,3-d]pyrimidine amides as potent Notum inhibitors. Bioorg.Med.Chem.Lett. (2020)

Release Date

2020-01-01

Peptides

Palmitoleoyl-protein carboxylesterase NOTUM: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Palmitoleoyl-protein carboxylesterase NOTUM

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