SMTL ID : 7bm3.1

Notum Rosmarinic acid complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

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

SO4.1: 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.122 Water bridges: A:R.56, A:R.56, A:K.120, A:Y.123 Salt bridges: A:R.56 SO4.4: 6 residues within 4Å: Chain A: P.93, Y.94, W.95, W.96, N.97, A.98 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.93, A:W.96, A:N.97 Water bridges: A:R.42, A:N.97 SO4.5: 5 residues within 4Å: Chain A: D.166, P.226, E.227, R.228 Ligands: SO4.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.166, A:E.227, A:R.228 Water bridges: A:C.229 Salt bridges: A:R.228 SO4.6: 3 residues within 4Å: Chain A: L.175, G.176, Y.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.177 Water bridges: A:Y.177 SO4.7: 6 residues within 4Å: Chain A: R.167, E.170, V.225, E.227, R.230 Ligands: SO4.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.225, A:E.227 Salt bridges: A:R.167, A:R.230 SO4.8: 1 residues within 4Å: Chain A: R.68 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.68 SO4.9: 4 residues within 4Å: Chain A: R.13, K.35, E.36, R.38 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.36, A:E.36, A:E.36 Water bridges: A:R.13, A:R.13 Salt bridges: A:R.13, A:R.38 SO4.10: 3 residues within 4Å: Chain A: Y.197, R.198, L.283 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.197 Water bridges: A:Y.197, A:R.198 Salt bridges: A:R.198

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

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

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

EDO.11: 5 residues within 4Å: Chain A: Y.33, W.75, P.76, R.79, P.104 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.33, A:R.79 EDO.12: 9 residues within 4Å: Chain A: L.192, D.193, N.194, P.210, T.211, F.243, V.269, D.270 Ligands: ROA.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.194 EDO.13: 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.14: 5 residues within 4Å: Chain A: E.264, L.310, S.311, H.312, P.373 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.264, A:H.312, A:P.373

3 x ROA: (2R)-3-(3,4-dihydroxyphenyl)-2-{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}propanoic acid(Non-covalent)

ROA.15: 15 residues within 4Å: Chain A: G.50, W.51, Y.52, S.155, A.156, F.191, P.210, T.211, I.214, F.243, E.264, A.265, T.268, H.312 Ligands: EDO.12 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.51, A:W.51, A:F.191, A:F.191, A:A.265 Hydrogen bonds: A:G.50, A:W.51, A:Y.52, A:Y.52, A:S.155, A:A.156, A:P.210, A:E.264 Salt bridges: A:H.312 ROA.16: 6 residues within 4Å: Chain A: D.322, Q.324, G.327, P.370, S.371 Ligands: ROA.17 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.370 Hydrogen bonds: A:D.322, A:G.327 Water bridges: A:D.322, A:Q.324 ROA.17: 9 residues within 4Å: Chain A: Q.324, V.325, K.326, G.327, D.361, C.368, N.369, P.370 Ligands: ROA.16 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.370 Hydrogen bonds: A:Q.324, A:K.326, A:G.327, A:D.361, A:N.369

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Notum Inhibitor. 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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