SMTL ID : 6r8p.1

Notum fragment 723

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: N.19, V.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.19 Water bridges: A:E.133

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: G.50, W.51, S.155, A.156, H.312, E.313 Ligands: JVB.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.50, A:W.51, A:S.155, A:A.156 GOL.3: 4 residues within 4Å: Chain A: I.316, R.317, S.318, H.319 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.318, A:S.318, A:H.319, A:H.319

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

SO4.4: 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:E.122 Water bridges: A:R.56, A:R.56, A:Y.123 Salt bridges: A:R.56 SO4.5: 6 residues within 4Å: Chain A: R.42, P.93, Y.94, W.95, W.96, N.97 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.96, A:N.97, A:A.98 Salt bridges: A:R.42 SO4.6: 4 residues within 4Å: Chain A: V.279, Q.280, E.281, R.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.281 Salt bridges: A:R.284 SO4.7: 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 SO4.8: 6 residues within 4Å: Chain A: R.167, E.170, V.225, P.226, E.227, R.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.227, A:R.230 Salt bridges: A:R.167 SO4.9: 6 residues within 4Å: Chain A: Y.33, E.48, W.75, R.79, F.102, P.104 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.79 Water bridges: A:R.68 SO4.10: 4 residues within 4Å: Chain A: R.292, R.295, H.296, K.299 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.296, A:H.296 Salt bridges: A:R.295, A:H.296 SO4.11: 4 residues within 4Å: Chain A: S.40, R.41, R.42, K.147 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.41 Salt bridges: A:R.42, A:K.147 SO4.12: 5 residues within 4Å: Chain A: R.13, L.34, K.35, E.36, R.38 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.36, A:E.36, A:E.36 Salt bridges: A:R.13, A:R.38 SO4.13: 2 residues within 4Å: Chain A: P.76, R.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.77 SO4.14: 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 SO4.15: 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

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

DMS.16: 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

1 x JVB: 2-(2-methylphenoxy)-~{N}-pyridin-3-yl-ethanamide(Non-covalent)

JVB.17: 9 residues within 4Å: Chain A: W.51, Y.52, T.159, F.191, P.210, F.242, F.243, V.269 Ligands: GOL.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.51, A:T.159, A:F.191, A:F.191, A:P.210, A:F.242, A:F.243, A:V.269 Hydrogen bonds: A:W.51 pi-Stacking: A:W.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Atkinson, B.N. et al., Discovery of 2-phenoxyacetamides as inhibitors of the Wnt-depalmitoleating enzyme NOTUM from an X-ray fragment screen. Medchemcomm (2019)

Release Date

2019-05-08

Peptides

Palmitoleoyl-protein carboxylesterase NOTUM: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Palmitoleoyl-protein carboxylesterase NOTUM

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