SMTL ID : 7b8o.1

Notum-Fragment 199

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

7 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 SO4.3: 3 residues within 4Å: Chain A: R.295, K.326, V.360 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.360 Water bridges: A:K.326, A:V.360 Salt bridges: A:R.295, A:K.326 SO4.4: 1 residues within 4Å: Chain A: K.120 No protein-ligand interaction detected (PLIP) SO4.5: 5 residues within 4Å: Chain A: R.56, K.120, N.121, E.122, Y.220 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.122, A:Y.220 Water bridges: A:R.56, A:Y.123, A:Y.123 Salt bridges: A:R.56 SO4.6: 4 residues within 4Å: Chain A: V.279, Q.280, E.281, R.284 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.280, A:E.281 Salt bridges: A:R.284 SO4.7: 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 SO4.8: 4 residues within 4Å: Chain A: R.167, E.170, V.225, E.227 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.170, A:V.225, A:E.227 Salt bridges: A:R.167

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

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

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

EDO.9: 2 residues within 4Å: Chain A: Y.197, R.198 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.197, A:R.198, A:R.198 Water bridges: A:Y.197 EDO.10: 4 residues within 4Å: Chain A: L.34, E.36, R.141 Ligands: SO4.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.36, A:E.36, A:R.141 EDO.11: 6 residues within 4Å: Chain A: Y.248, L.251, R.252, S.253, P.254, V.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.252, A:V.255, A:V.255 EDO.12: 3 residues within 4Å: Chain A: S.40, R.41, R.42 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.41, A:R.42, A:R.42

1 x T1W: [(2~{S})-2-methylpiperidin-1-yl]-morpholin-4-yl-methanone(Non-covalent)

T1W.13: 9 residues within 4Å: Chain A: W.51, Y.52, V.110, S.155, A.156, T.159, F.191, P.210, F.243 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.51, A:Y.52, A:V.110, A:A.156, A:F.191 Hydrogen bonds: A:Y.52

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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