SMTL ID : 6r8r.1

Structure of the Wnt deacylase Notum in complex with isoquinoline 45

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

monomer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.19, S.21, V.22, L.129, R.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.19 Water bridges: A:E.133

1 x JV8: ~{N}-isoquinolin-6-yl-2-(2-methylphenoxy)ethanamide(Non-covalent)

JV8.2: 11 residues within 4Å: Chain A: W.51, Y.52, V.110, T.159, F.191, P.210, I.214, F.243, T.268, V.269 Ligands: SO4.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.51, A:V.110, A:F.191, A:P.210, A:I.214, A:F.243, A:V.269 Water bridges: A:Y.52 pi-Stacking: A:W.51, A:W.51, A:W.51, A:F.191

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

SO4.3: 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 SO4.4: 3 residues within 4Å: Chain A: R.295, H.296, K.299 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.296, A:H.296 Salt bridges: A:H.296, A:K.299 SO4.5: 3 residues within 4Å: Chain A: R.332, H.335, R.339 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.339 Salt bridges: A:R.332, A:H.335, A:R.339 SO4.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.7: 7 residues within 4Å: Chain A: G.50, W.51, S.155, A.156, F.191, H.312 Ligands: JV8.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.50, A:W.51, A:S.155, A:S.155, A:A.156 Salt bridges: A:H.312 SO4.8: 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, A:Y.220 Water bridges: A:R.56, A:Y.123 Salt bridges: A:R.56 SO4.9: 5 residues within 4Å: Chain A: R.167, E.170, V.225, E.227, R.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.227 Salt bridges: A:R.167, A:R.230 SO4.10: 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

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

DMS.11: 6 residues within 4Å: Chain A: R.42, 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.12: 6 residues within 4Å: Chain A: Y.248, L.251, R.252, S.253, P.254, V.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.255 DMS.13: 7 residues within 4Å: Chain A: Y.33, E.48, 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.14: 3 residues within 4Å: Chain A: R.317, S.318, H.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.319, A:H.319 DMS.15: 2 residues within 4Å: Chain A: K.326, V.360 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.326 Water bridges: A:V.360

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

EDO.16: 8 residues within 4Å: Chain A: W.51, Y.52, C.53, N.58, R.62, M.66, T.205 Ligands: EDO.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.62 EDO.17: 7 residues within 4Å: Chain A: R.79, T.80, G.81, T.82, L.85, F.102, I.316 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.79, A:R.79, A:T.82, A:T.82 EDO.18: 2 residues within 4Å: Chain A: S.144, Y.177 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.177, A:Y.177 EDO.19: 9 residues within 4Å: Chain A: L.192, D.193, N.194, Q.196, A.209, P.210, T.211, V.269, D.270 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.196, A:T.211, A:T.211, A:D.270, A:D.270 EDO.20: 5 residues within 4Å: Chain A: D.26, Y.63, K.117, E.122, Y.123 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.117, A:K.117, A:E.122, A:Y.123 EDO.21: 6 residues within 4Å: Chain A: W.190, Y.245, Y.248, P.249, T.297, V.301 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.245 EDO.22: 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:Q.324, A:K.326 EDO.23: 5 residues within 4Å: Chain A: S.115, N.121, R.219, Y.220, N.222 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.121 Water bridges: A:K.120, A:N.121 EDO.24: 5 residues within 4Å: Chain A: S.61, R.62, T.65, M.66 Ligands: EDO.16 No protein-ligand interaction detected (PLIP) EDO.25: 2 residues within 4Å: Chain A: T.200, D.201 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Atkinson, B.N. et al., Discovery of 2-phenoxyacetamides as inhibitors of the Wnt-depalmitoleating enzyme NOTUM from an X-ray fragment screen. Medchemcomm (2019)

Release Date

2019-05-08

Peptides

Palmitoleoyl-protein carboxylesterase NOTUM: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Palmitoleoyl-protein carboxylesterase NOTUM

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