SMTL ID : 7arg.1

Notum in complex with ARUK3002704

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

monomer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.19, V.22, Q.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.19, A:Q.132 Water bridges: A:E.133

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

SO4.2: 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 SO4.3: 3 residues within 4Å: Chain A: R.332, H.335, R.339 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.339 Salt bridges: A:R.332, A:H.335, A:R.339 SO4.4: 5 residues within 4Å: Chain A: R.56, K.120, N.121, E.122, Y.220 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.122, A:Y.220 Water bridges: A:Y.123 Salt bridges: A:R.56 SO4.5: 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 SO4.9: 3 residues within 4Å: Chain A: Y.197, R.198, L.283 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.280 Salt bridges: A:R.198 SO4.10: 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 DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 6 residues within 4Å: Chain A: Y.248, L.251, R.252, S.253, P.254, V.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.255

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

EDO.7: 7 residues within 4Å: Chain A: R.79, T.80, G.81, T.82, L.85, F.102, I.316 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.79, A:R.79, A:T.82, A:T.82 EDO.8: 5 residues within 4Å: Chain A: D.26, Y.63, K.117, E.122, Y.123 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.117, A:K.117, A:E.122, A:Y.123 EDO.11: 3 residues within 4Å: Chain A: R.295, H.296, K.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.299 Water bridges: A:R.295 EDO.12: 6 residues within 4Å: Chain A: R.42, Y.94, W.95, W.96, N.97, A.98 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.95, A:N.97 EDO.13: 3 residues within 4Å: Chain A: L.175, G.176, Y.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.176

1 x RW8: methyl 4-(2,3-dihydroindol-1-yl)-4-oxidanylidene-butanoate(Covalent)

RW8.14: 12 residues within 4Å: Chain A: G.49, G.50, W.51, Y.52, S.155, A.156, T.159, F.191, P.210, I.214, F.242, A.265 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.51, A:T.159, A:F.191, A:F.191, A:F.191, A:F.191, A:P.210, A:I.214, A:A.265 Hydrogen bonds: A:G.50, A:W.51, A:A.156 pi-Stacking: A:Y.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Structural Insights into Notum Covalent Inhibition. J.Med.Chem. (2021)

Release Date

2021-08-04

Peptides

Palmitoleoyl-protein carboxylesterase NOTUM: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Palmitoleoyl-protein carboxylesterase NOTUM

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