SMTL ID : 6yxi.1

Structure of Notum in complex with a 1-(3-Chlorophenyl)-2,5-dimethyl-1H-pyrrole-3-carboxylic acid inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

monomer

Ligands

1 x PZ8: 1-(3-chlorophenyl)-2,5-dimethyl-pyrrole-3-carboxylic acid(Non-covalent)

PZ8.1: 11 residues within 4Å: Chain A: W.51, Y.52, A.156, F.191, L.192, P.210, T.211, I.214, F.243, A.265, V.269 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.51, A:F.191, A:F.191, A:P.210, A:T.211, A:I.214, A:I.214, A:V.269 Hydrogen bonds: A:W.51, A:A.156 pi-Stacking: A:Y.52, A:F.191 Halogen bonds: A:L.192

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

NAG.2: 3 residues within 4Å: Chain A: N.19, V.22, R.136 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.19, A:R.136, A:R.136

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

DMS.3: 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

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

SO4.4: 4 residues within 4Å: Chain A: T.65, M.66, R.67, R.68 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.67, A:R.68 Water bridges: A:M.66, A:R.68, A:R.68, A:L.69 Salt bridges: A:R.68 SO4.5: 5 residues within 4Å: Chain A: R.56, K.120, N.121, E.122, Y.220 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.120, A:E.122, A:Y.220, A:Y.220 Water bridges: A:Y.123, A:Y.123 Salt bridges: A:R.56 SO4.6: 2 residues within 4Å: Chain A: R.228, R.231 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.231 Water bridges: A:R.228 Salt bridges: A:R.228 SO4.7: 4 residues within 4Å: Chain A: R.13, L.34, K.35, E.36 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.34, A:E.36 Salt bridges: A:R.13 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: 3 residues within 4Å: Chain A: Y.197, R.198, L.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.197 Water bridges: A:Q.280 Salt bridges: A:R.198 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

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

EDO.11: 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:Y.33, A:Y.33, A:R.79 Water bridges: A:R.79 EDO.12: 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:H.296, A:K.299

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

2020-08-19

Peptides

Palmitoleoyl-protein carboxylesterase NOTUM: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Palmitoleoyl-protein carboxylesterase NOTUM

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