SMTL ID : 7b8n.1

Notum-Fragment 197

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

monomer

Ligands

6 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 SO4.4: 2 residues within 4Å: Chain A: K.326, V.360 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.360 Water bridges: A:K.326, A:K.326 Salt bridges: A:K.326 SO4.5: 5 residues within 4Å: Chain A: R.56, K.120, N.121, E.122, Y.220 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.122 Water bridges: A:R.56, A:Y.123, A:Y.123 Salt bridges: A:R.56 SO4.6: 6 residues within 4Å: Chain A: R.42, P.93, Y.94, W.95, W.96, N.97 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.93, A:W.96, A:N.97 Salt bridges: A:R.42 SO4.7: 1 residues within 4Å: Chain A: R.228 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.231 Salt bridges: A:R.228 SO4.8: 3 residues within 4Å: Chain A: H.15, R.141 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.15, A:R.141

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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.19, A:R.136

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: Y.248, L.251, R.252, S.253, P.254, V.255 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.248, A:R.252, A:V.255, A:V.255 Water bridges: A:Y.248, A:L.251

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

EDO.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, A:R.198, A:R.198 EDO.10: 3 residues within 4Å: Chain A: E.36, R.38 Ligands: SO4.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.36, A:R.38 EDO.11: 5 residues within 4Å: Chain A: G.39, S.40, R.41, R.42, N.97 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.41, A:R.42, A:N.97 EDO.12: 7 residues within 4Å: Chain A: L.192, D.193, N.194, A.209, P.210, T.211, D.270 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.211, A:T.211

1 x T2E: 5-azanyl-2-(pyridin-3-ylmethylamino)benzoic acid(Non-covalent)

T2E.13: 9 residues within 4Å: Chain A: G.50, W.51, Y.52, S.155, A.156, T.159, F.191, A.265, H.312 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.51, A:Y.52, A:A.265 Hydrogen bonds: A:G.50, A:W.51, A:S.155, A:A.156 Salt bridges: A:H.312 pi-Stacking: A:F.191

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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