SMTL ID : 6yv0.1

STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH A PYRROLIDINE-3-CARBOXYLIC ACID FRAGMENT 587

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: T.65, M.66, R.67, R.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.67, A:R.68 Salt bridges: A:R.68

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

EDO.2: 2 residues within 4Å: Chain A: L.175, Y.177 No protein-ligand interaction detected (PLIP) EDO.3: 5 residues within 4Å: Chain A: Y.248, L.251, S.253, P.254, V.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.251, A:V.255 EDO.4: 5 residues within 4Å: Chain A: E.313, I.314, R.317, H.319, W.320 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.313, A:H.319 EDO.5: 3 residues within 4Å: Chain A: S.40, R.41, R.42 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.41, A:R.42

1 x PQT: (3~{R})-1-(2-chlorophenyl)pyrrolidine-3-carboxylic acid(Non-covalent)

PQT.6: 12 residues within 4Å: Chain A: W.51, Y.52, V.110, S.155, A.156, T.159, F.191, P.210, I.214, F.242, A.265, H.312 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.51, A:V.110, A:T.159, A:F.191, A:I.214, A:A.265 Hydrogen bonds: A:W.51, A:A.156 Water bridges: A:S.155, A:S.155 Salt bridges: A:H.312 pi-Stacking: A:F.191

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

NAG.7: 4 residues within 4Å: Chain A: N.19, V.22, L.129, R.136 No protein-ligand interaction detected (PLIP)

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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