SMTL ID : 7b3g.1

Notum complex with ARUK3003902

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

monomer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: N.19, V.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.19, A:R.136

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

SO4.2: 5 residues within 4Å: Chain A: R.56, K.120, N.121, E.122, Y.220 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.120, A:E.122, A:Y.220, A:Y.220 Water bridges: A:R.56, A:Y.123, A:Y.123 Salt bridges: A:R.56 SO4.3: 6 residues within 4Å: Chain A: R.167, E.170, V.225, E.227, R.230 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.170 Salt bridges: A:R.167, A:R.230 SO4.4: 2 residues within 4Å: Chain A: R.228, R.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.231 Salt bridges: A:R.228 SO4.11: 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 SO4.12: 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 SO4.13: 3 residues within 4Å: Chain A: Y.197, R.198, L.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.197 Salt bridges: A:R.198 SO4.14: 2 residues within 4Å: Chain A: R.339, H.342 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.339, A:H.342

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

DMS.5: 5 residues within 4Å: Chain A: Y.94, W.95, W.96, N.97, A.98 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.97 pi-Cation interactions: A:W.96 DMS.9: 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 DMS.10: 5 residues within 4Å: Chain A: Y.33, W.75, P.76, R.79, P.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.79 Salt bridges: A:E.48 pi-Cation interactions: A:W.75

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

EDO.6: 3 residues within 4Å: Chain A: R.295, H.296, K.299 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.296 EDO.7: 5 residues within 4Å: Chain A: D.166, R.167, P.226, E.227 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.167, A:E.227

1 x SSQ: 6-((2-chlorophenyl)thio)-[1,2,4]triazolo[4,3-b]pyridazin-3(2H)-one(Non-covalent)

SSQ.8: 13 residues within 4Å: Chain A: G.50, W.51, Y.52, V.110, S.155, A.156, T.159, F.191, P.210, F.242, F.243, A.265, H.312 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:T.159, A:F.191, A:F.191, A:A.265 Hydrogen bonds: A:G.50, A:W.51, A:A.156, A:H.312 Water bridges: A:S.155, A:S.155, A:S.155 pi-Stacking: A:W.51, A:W.51, A:W.51, A:F.191, A:F.243 Halogen bonds: A:Y.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Steadman, D. et al., Virtual Screening Directly Identifies New Fragment-Sized Inhibitors of Carboxylesterase Notum with Nanomolar Activity. J.Med.Chem. (2022)

Release Date

2021-12-08

Peptides

Palmitoleoyl-protein carboxylesterase NOTUM: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Palmitoleoyl-protein carboxylesterase NOTUM

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