SMTL ID : 6zvl.1

ARUK3000263 complex with Notum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: N.19, S.21, V.22, M.126, L.129, R.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.19, A:R.136

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

SO4.2: 4 residues within 4Å: Chain A: R.332, H.335, R.339, C.355 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.332, A:H.335, A:R.339 SO4.3: 6 residues within 4Å: Chain A: R.56, K.120, N.121, E.122, Y.123, Y.220 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.120, A:E.122, A:Y.220 Water bridges: A:Y.123 Salt bridges: A:R.56 SO4.4: 6 residues within 4Å: Chain A: R.167, E.170, V.225, P.226, 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 SO4.5: 3 residues within 4Å: Chain A: R.228, R.231, R.252 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.231, A:R.252 Salt bridges: A:R.228

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

DMS.6: 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.7: 6 residues within 4Å: Chain A: Y.248, L.251, R.252, S.253, P.254, V.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.248, A:V.255

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

EDO.8: 9 residues within 4Å: Chain A: W.260, E.313, I.314, R.317, H.319, W.320, D.322, V.323, P.373 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.317, A:H.319, A:V.323

1 x QR2: 5-[4-chloranyl-3-(trifluoromethyl)phenyl]-3~{H}-1,3,4-oxadiazol-2-one(Non-covalent)

QR2.9: 15 residues within 4Å: Chain A: G.50, W.51, Y.52, V.110, S.155, A.156, T.159, F.191, P.210, I.214, F.242, F.243, A.265, V.269, H.312 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.51 Hydrogen bonds: A:G.50, A:W.51, A:A.156, A:H.312 Water bridges: A:S.155, A:S.155 pi-Stacking: A:W.51, A:W.51, A:F.191 Halogen bonds: A:F.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mahy, W. et al., 5-Phenyl-1,3,4-oxadiazol-2(3 H )-ones Are Potent Inhibitors of Notum Carboxylesterase Activity Identified by the Optimization of a Crystallographic Fragment Screening Hit. J.Med.Chem. (2020)

Release Date

2020-11-11

Peptides

Palmitoleoyl-protein carboxylesterase NOTUM: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Palmitoleoyl-protein carboxylesterase NOTUM

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