SMTL ID : 7b2y.1

Notum complex with ARUK3003910

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.23 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.19, A:R.136

7 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: 6 residues within 4Å: Chain A: R.167, E.170, V.225, E.227, R.230 Ligands: EDO.9 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: 3 residues within 4Å: Chain A: R.228, R.231, R.252 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.231, A:R.252 Salt bridges: A:R.228 SO4.12: 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 SO4.13: 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 SO4.14: 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:Q.280 Salt bridges: A:R.198 SO4.15: 3 residues within 4Å: Chain A: P.356, V.357, H.358 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.357, A:H.358 Water bridges: A:L.352, A:L.352, A:C.355

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

DMS.5: 6 residues within 4Å: Chain A: R.42, Y.94, W.95, W.96, N.97, A.98 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.42, A:R.42, A:N.97, A:A.98 pi-Cation interactions: A:W.96

1 x SRQ: 2,2-bis(fluoranyl)ethyl 4-(2,3-dihydroindol-1-yl)-4-oxidanylidene-butanoate(Covalent)

SRQ.6: 10 residues within 4Å: Chain A: G.49, G.50, W.51, Y.52, S.155, A.156, T.159, F.191, A.265, H.312 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.51, A:F.191, A:F.191, A:F.191, A:F.191, A:A.265 Hydrogen bonds: A:G.50, A:W.51, A:A.156 Water bridges: A:G.49 pi-Stacking: A:Y.52

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

EDO.7: 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.8: 8 residues within 4Å: Chain A: L.192, D.193, N.194, A.209, P.210, T.211, V.269, D.270 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.211, A:T.211, A:D.270 EDO.9: 6 residues within 4Å: Chain A: D.166, R.167, E.170, P.226, E.227 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.167, A:E.227 EDO.10: 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 GOL: GLYCEROL(Non-functional Binders)

GOL.11: 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:L.251, A:R.252, A:V.255, A:V.255 Water bridges: A:L.251

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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