SMTL ID : 7b9i.1

Notum Fragment 297

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

monomer

Ligands

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

SO4.1: 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:R.67, A:R.68 Water bridges: A:D.74 Salt bridges: A:R.68 SO4.5: 3 residues within 4Å: Chain A: R.295, K.326, V.360 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.360 Water bridges: A:R.295, A:K.326, A:V.360 Salt bridges: A:R.295, A:K.326 SO4.6: 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:E.122 Water bridges: A:R.56, A:R.56, A:K.120, A:Y.123, A:Y.123 Salt bridges: A:R.56, A:K.120 SO4.7: 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 SO4.8: 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

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, L.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.19

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

DMS.3: 3 residues within 4Å: Chain A: L.175, G.176, Y.177 No protein-ligand interaction detected (PLIP) DMS.4: 5 residues within 4Å: Chain A: R.42, Y.94, W.95, W.96, N.97 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.97, A:A.98 pi-Cation interactions: A:W.96

2 x T3T: 1-(1,3-benzodioxol-5-yl)-~{N}-(pyridin-2-ylmethyl)methanamine(Covalent)(Non-covalent)

T3T.9: 12 residues within 4Å: Chain A: G.49, G.50, W.51, Y.52, S.155, A.156, F.191, P.210, F.242, F.243, H.312, E.313 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.50, A:W.51, A:A.156 pi-Stacking: A:Y.52, A:F.191 pi-Cation interactions: A:H.312 T3T.10: 7 residues within 4Å: Chain A: D.26, S.28, Y.63, R.73, K.117, E.122, Y.123 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.26 Hydrogen bonds: A:R.73, A:K.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Structural Analysis and Development of Notum Fragment Screening Hits. Acs Chem Neurosci (2022)

Release Date

2022-01-12

Peptides

Palmitoleoyl-protein carboxylesterase NOTUM: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Palmitoleoyl-protein carboxylesterase NOTUM

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