SMTL ID : 7b37.1

Notum complex with ARUK3003718

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

monomer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.19, S.21, V.22, L.129, R.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.19

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

SO4.2: 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:K.120, A:E.122, A:Y.220 Water bridges: A:Y.123 Salt bridges: A:R.56 SO4.3: 5 residues within 4Å: Chain A: R.167, E.170, V.225, E.227, R.230 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.227, A:E.227 Salt bridges: A:R.167, A:R.230 SO4.4: 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 SO4.11: 4 residues within 4Å: Chain A: T.65, M.66, R.67, R.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.67, A:R.68 Salt bridges: A:R.68

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

DMS.5: 5 residues within 4Å: Chain A: Y.94, W.95, W.96, N.97, A.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.97, A:A.98 pi-Cation interactions: A:W.96 DMS.9: 6 residues within 4Å: Chain A: Y.248, L.251, R.252, S.253, P.254, V.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.248, A:V.255 DMS.10: 7 residues within 4Å: Chain A: L.192, D.193, N.194, A.209, P.210, T.211, D.270 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.194

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

EDO.6: 3 residues within 4Å: Chain A: R.295, H.296, K.299 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.295, A:H.296, A:K.299 Water bridges: A:R.295 EDO.7: 5 residues within 4Å: Chain A: K.299, D.300, V.301, P.302, H.358 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.300

1 x SRK: 4-(2,3-dihydroindol-1-yl)-4-oxidanylidene-butanoic acid(Non-covalent)

SRK.8: 12 residues within 4Å: Chain A: G.50, W.51, Y.52, S.155, A.156, T.159, F.191, P.210, I.214, F.242, A.265, H.312 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.51, A:W.51, A:T.159, A:F.191, A:F.191, A:F.191, A:P.210, A:P.210, A:I.214, A:A.265 Hydrogen bonds: A:G.50, A:W.51, A:A.156 Water bridges: A:S.155, A:S.155 Salt bridges: A:H.312

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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