SMTL ID : 7bo2.1

Notum Fragment_130 (4H-thieno[3,2-c]chromene-2-carboxylic acid)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.21 Å

Oligo State

monomer

Ligands

6 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:T.65, A:R.67, A:R.68 Water bridges: 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.122 Water bridges: A:R.56, A:Y.123 Salt bridges: A:R.56 SO4.4: 2 residues within 4Å: Chain A: P.76, R.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.77 SO4.5: 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 SO4.6: 3 residues within 4Å: Chain A: V.279, Q.280, E.281 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.281 SO4.7: 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 NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 5 residues within 4Å: Chain A: N.19, S.21, V.22, E.133, R.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.19 Water bridges: A:E.133

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

EDO.8: 3 residues within 4Å: Chain A: L.175, G.176, Y.177 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain A: R.13, K.35, E.36, R.38 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.36, A:E.36, A:E.36, A:R.38 EDO.10: 4 residues within 4Å: Chain A: Y.33, W.75, P.76, R.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.33, A:R.79 EDO.11: 9 residues within 4Å: Chain A: L.192, D.193, N.194, Q.196, A.209, P.210, T.211, V.269, D.270 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.211, A:T.211, A:D.270, A:D.270 EDO.12: 3 residues within 4Å: Chain A: R.317, S.318, H.319 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.317, A:S.318, A:H.319, A:H.319 EDO.13: 6 residues within 4Å: Chain A: Y.248, L.251, R.252, S.253, P.254, V.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.251, A:V.255, A:V.255 EDO.14: 7 residues within 4Å: Chain A: R.79, T.80, G.81, T.82, L.85, F.102, I.316 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.79, A:T.82, A:T.82 Water bridges: A:T.80, A:T.80

1 x U62: 4~{H}-thieno[3,2-c]chromene-2-carboxylic acid(Non-covalent)

U62.15: 11 residues within 4Å: Chain A: G.50, W.51, S.155, A.156, T.159, F.191, I.214, F.242, A.265, V.269, H.312 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.51, A:W.51, A:F.191, A:F.191, A:F.191, A:I.214, A:A.265 Hydrogen bonds: A:G.50, A:W.51, A:S.155, A:A.156 Salt bridges: A:H.312 pi-Stacking: A:F.191

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

DMS.16: 2 residues within 4Å: Chain A: Y.197, R.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.198, A:R.198 Water bridges: A:Y.197 DMS.17: 5 residues within 4Å: Chain A: D.26, Y.63, K.117, E.122, Y.123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.117 Salt bridges: A:E.122 pi-Cation interactions: A:Y.63 DMS.18: 5 residues within 4Å: Chain A: R.42, Y.94, W.95, W.96, N.97 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.97, A:A.98 pi-Cation interactions: A:W.96

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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