SMTL ID : 7bmd.1

Notum TDZD8 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: R.167, E.170, V.225, E.227, R.230 Ligands: GOL.15 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.167, A:R.230 SO4.2: 4 residues within 4Å: Chain A: T.65, M.66, R.67, R.68 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.67, A:R.68 Water bridges: A:D.74, A:D.74 Salt bridges: A:R.68 SO4.3: 5 residues within 4Å: Chain A: R.56, K.120, N.121, E.122, Y.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.122 Water bridges: A:Y.123 Salt bridges: A:R.56 SO4.4: 4 residues within 4Å: Chain A: R.13, L.34, K.35, E.36 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.36, A:E.36, A:E.36 Salt bridges: A:R.13 SO4.5: 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 SO4.6: 6 residues within 4Å: Chain A: W.51, Y.52, S.155, A.156, F.191 Ligands: U3W.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.51, A:S.155, A:A.156 SO4.7: 7 residues within 4Å: Chain A: R.42, Y.94, W.95, W.96, N.97, A.98 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.93, A:W.96, A:N.97 SO4.8: 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 SO4.9: 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 Water bridges: A:Y.197 Salt bridges: A:R.198 SO4.10: 5 residues within 4Å: Chain A: Y.33, E.48, W.75, P.76, P.104 No protein-ligand interaction detected (PLIP) SO4.11: 2 residues within 4Å: Chain A: P.76, R.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.77

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 7 residues within 4Å: Chain A: G.39, S.40, R.41, R.42, N.97, K.147 Ligands: SO4.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.41, A:R.42, A:N.97, A:N.97, A:K.147 GOL.13: 3 residues within 4Å: Chain A: R.339, H.342, L.352 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.339 GOL.14: 3 residues within 4Å: Chain A: R.317, S.318, H.319 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.317, A:R.317, A:S.318, A:S.318, A:H.319, A:H.319 GOL.15: 8 residues within 4Å: Chain A: D.166, E.170, P.226, E.227, R.228, T.250, L.251 Ligands: SO4.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.166, A:E.170, A:E.227, A:R.228, A:R.228 Water bridges: A:P.226, A:T.250

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

NAG.16: 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 Water bridges: A:E.133

1 x U3W: 2-methyl-4-(phenylmethyl)-1,2,4-thiadiazolidine-3,5-dione(Non-covalent)

U3W.17: 11 residues within 4Å: Chain A: W.51, Y.52, T.159, F.191, L.192, I.214, F.242, F.243, Q.266, V.269 Ligands: SO4.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.52, A:T.159, A:I.214, A:I.214, A:F.242, A:F.243 pi-Stacking: A:F.191

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

DMS.18: 4 residues within 4Å: Chain A: P.351, P.356, V.357, H.358 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.357, A:H.358

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Notum Inhibitor TDZD8. To Be Published

Release Date

2022-03-02

Peptides

Palmitoleoyl-protein carboxylesterase NOTUM: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Palmitoleoyl-protein carboxylesterase NOTUM

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