SMTL ID : 6t2h.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

monomer

Ligands

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

DMS.1: 8 residues within 4Å: Chain A: Y.33, E.48, R.68, W.75, P.76, R.79, F.102, P.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.79 Salt bridges: A:E.48 pi-Cation interactions: A:W.75 DMS.2: 4 residues within 4Å: Chain A: L.16, S.72, R.73, W.75 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.75

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

SO4.3: 6 residues within 4Å: Chain A: R.56, K.120, N.121, E.122, Y.220 Ligands: EDO.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.122, A:Y.220 Water bridges: A:Y.123 Salt bridges: A:R.56 SO4.4: 3 residues within 4Å: Chain A: V.279, Q.280, E.281 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.280, A:E.281, A:E.281 SO4.5: 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 SO4.6: 1 residues within 4Å: Chain A: R.68 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.68 SO4.7: 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 SO4.8: 4 residues within 4Å: Chain A: R.167, E.170, V.225, E.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.227 Salt bridges: A:R.167 SO4.9: 4 residues within 4Å: Chain A: R.13, L.34, K.35, E.36 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.36, A:E.36, A:E.36 Salt bridges: A:R.13

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

EDO.10: 2 residues within 4Å: Chain A: L.175, Y.177 No protein-ligand interaction detected (PLIP) EDO.11: 5 residues within 4Å: Chain A: Y.248, L.251, S.253, P.254, V.255 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.251, A:V.255, A:V.255 Water bridges: A:Y.248, A:L.251 EDO.12: 7 residues within 4Å: Chain A: R.42, Y.94, W.95, W.96, N.97, A.98 Ligands: EDO.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.42, A:W.95, A:N.97, A:A.98 EDO.13: 8 residues within 4Å: Chain A: R.79, T.80, G.81, T.82, L.85, F.102, I.316 Ligands: EDO.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.79, A:R.79, A:T.82, A:T.82 EDO.14: 2 residues within 4Å: Chain A: P.76, R.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.77 EDO.15: 6 residues within 4Å: Chain A: R.42, P.93, Y.94, H.335, D.338 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.42, A:R.42, A:P.93 EDO.16: 3 residues within 4Å: Chain A: R.295, H.296, K.299 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.295, A:K.299 Water bridges: A:R.295 EDO.17: 5 residues within 4Å: Chain A: G.39, S.40, R.41, R.42, K.147 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.41, A:N.97, A:K.147 EDO.18: 2 residues within 4Å: Chain A: R.56 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.56 Water bridges: A:R.56, A:E.57 EDO.19: 4 residues within 4Å: Chain A: D.193, N.194, Y.245, E.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.245, A:E.293 EDO.20: 3 residues within 4Å: Chain A: R.79, T.80 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.79, A:T.80, A:T.80 EDO.21: 3 residues within 4Å: Chain A: R.317, S.318, H.319 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.317, A:H.319, A:H.319 EDO.22: 5 residues within 4Å: Chain A: Y.245, Y.248, P.249, T.297, V.301 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.245

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

NAG.23: 2 residues within 4Å: Chain A: N.19, V.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.19

1 x M9N: 2-[[(4~{S})-5-chloranyl-6-methyl-1,2,3,4-tetrahydrothieno[2,3-d]pyrimidin-4-yl]sulfanyl]ethanoic acid(Non-covalent)

M9N.24: 12 residues within 4Å: Chain A: G.50, W.51, V.110, S.155, A.156, T.159, F.191, P.210, F.242, A.265, V.269, H.312 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.242 Hydrogen bonds: A:G.50, A:W.51, A:W.51, A:S.155, A:A.156 Salt bridges: A:H.312 pi-Stacking: A:F.191

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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