SMTL ID : 6r8q.1

STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH A BENZOTRIAZOLE FRAGMENT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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, A:E.133

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

SO4.2: 8 residues within 4Å: Chain A: G.49, G.50, W.51, S.155, A.156, H.312, E.313 Ligands: JV5.15 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.50, A:W.51, A:S.155, A:S.155, A:A.156, A:E.313 Salt bridges: A:H.312 SO4.3: 4 residues within 4Å: Chain A: R.332, H.335, R.339, C.355 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.339 Salt bridges: A:R.332, A:H.335, A:R.339 SO4.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.5: 5 residues within 4Å: Chain A: R.56, K.120, N.121, E.122, Y.220 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.122 Water bridges: A:R.56, A:Y.123 Salt bridges: A:R.56 SO4.6: 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 SO4.7: 6 residues within 4Å: Chain A: P.93, Y.94, W.95, W.96, N.97, A.98 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.93, A:W.96, A:N.97, A:A.98 SO4.8: 5 residues within 4Å: Chain A: R.167, E.170, V.225, E.227, R.230 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.227 Water bridges: A:R.167, A:E.170 Salt bridges: A:R.167, A:R.230 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

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

EDO.10: 8 residues within 4Å: Chain A: Q.324, V.325, K.326, G.327, N.369, P.370, S.371 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.327 Water bridges: A:K.326 EDO.11: 4 residues within 4Å: Chain A: Q.324, P.370, S.371 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.324, A:P.370 EDO.12: 5 residues within 4Å: Chain A: Y.33, W.75, P.76, R.79, P.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.79 Water bridges: A:R.68, A:R.68, A:R.68 EDO.13: 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.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 JV5: ~{N}-(1~{H}-benzotriazol-5-yl)-2-(2-methylphenoxy)ethanamide(Non-covalent)

JV5.15: 13 residues within 4Å: Chain A: W.51, Y.52, S.155, A.156, T.159, F.191, P.210, I.214, F.242, F.243, A.265, V.269 Ligands: SO4.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.51, A:T.159, A:F.191, A:F.191, A:P.210, A:I.214, A:F.243, A:A.265, A:V.269 Hydrogen bonds: A:W.51, A:A.156 pi-Stacking: A:W.51, A:W.51, A:W.51, A:F.191

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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