SMTL ID : 6yv2.1

STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH A PYRROLIDINE-3-CARBOXYLIC ACID FRAGMENT 598

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.19, V.22, L.129, R.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.19

1 x PUE: (3~{R})-1-phenylpyrrolidine-3-carboxylic acid(Non-covalent)

PUE.2: 11 residues within 4Å: Chain A: W.51, Y.52, S.155, A.156, T.159, F.191, I.214, F.242, F.243, A.265, H.312 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.51, A:W.51, A:Y.52, A:T.159, A:F.191, A:F.191, A:I.214, A:F.243, A:A.265 Hydrogen bonds: A:G.50, A:W.51, A:A.156 Water bridges: A:S.155, A:S.155 Salt bridges: A:H.312 pi-Stacking: A:F.191

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

SO4.3: 2 residues within 4Å: Chain A: K.326, V.360 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.358 Salt bridges: A:K.326 SO4.4: 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:T.65, A:R.67, A:R.68 Salt bridges: A:R.68 SO4.5: 3 residues within 4Å: Chain A: R.332, R.339, C.355 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.332, A:R.339

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

EDO.6: 2 residues within 4Å: Chain A: L.175, G.176 No protein-ligand interaction detected (PLIP) EDO.7: 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 Water bridges: A:Y.248, A:Y.248, A:V.255 EDO.8: 5 residues within 4Å: Chain A: R.167, E.170, V.225, P.226, E.227 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.167, A:R.167, A:E.227 Water bridges: A:D.166, A:D.166, A:R.167, A:V.225, A:R.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mahy, W. et al., Screening of a Custom-Designed Acid Fragment Library Identifies 1-Phenylpyrroles and 1-Phenylpyrrolidines as Inhibitors of Notum Carboxylesterase Activity. J.Med.Chem. (2020)

Release Date

2020-05-13

Peptides

Palmitoleoyl-protein carboxylesterase NOTUM: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Palmitoleoyl-protein carboxylesterase NOTUM

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