SMTL ID : 5dyw.2 (1 other biounit)

Crystal structure of human butyrylcholinesterase in complex with N-((1-benzylpiperidin-3-yl)methyl)-N-(2-methoxyethyl)naphthalene-2-sulfonamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

3 x NAG- NAG- FUL: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUL.1: 9 residues within 4Å: Chain A: Y.238, N.242, N.246, L.250, F.279, V.280, V.281, P.282, Y.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.246, A:N.246, A:Y.283 NAG-NAG-FUL.2: 4 residues within 4Å: Chain A: E.256, N.257, T.259, E.260 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.256 NAG-NAG-FUL.3: 3 residues within 4Å: Chain A: K.428, D.455, N.456 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.456

1 x 5HF: N-{[(3S)-1-benzylpiperidin-3-yl]methyl}-N-(2-methoxyethyl)naphthalene-2-sulfonamide(Non-covalent)

5HF.4: 20 residues within 4Å: Chain A: N.69, I.70, D.71, W.83, G.117, G.118, Q.120, T.121, S.199, W.232, L.287, S.288, A.329, F.330, Y.333, F.399, W.431, M.438, H.439, Y.441 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.232, A:A.329, A:Y.333, A:F.399, A:W.431, A:Y.441 Hydrogen bonds: A:T.121 Water bridges: A:N.69 Salt bridges: A:D.71 pi-Stacking: A:W.83, A:F.330

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: L.19, Y.62, W.99, D.130, K.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.99, A:K.132 GOL.6: 4 residues within 4Å: Chain A: R.241, L.245, E.256, N.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.241 GOL.7: 3 residues within 4Å: Chain A: P.47, Q.48, S.49 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.48, A:S.49, A:S.49 GOL.8: 6 residues within 4Å: Chain A: W.232, T.285, L.287, S.288, V.289, N.398 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.285, A:L.287, A:V.289, A:N.398 Water bridges: A:N.398 GOL.9: 8 residues within 4Å: Chain A: P.450, E.452, R.453, D.455, N.456, Y.457, K.459, E.462 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.452, A:D.455, A:Y.457

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

EDO.10: 3 residues within 4Å: Chain A: R.43, E.91, K.268 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.43 Water bridges: A:G.40, A:E.91, A:E.91 EDO.11: 3 residues within 4Å: Chain A: R.348, Q.352, E.368 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.352 EDO.12: 4 residues within 4Å: Chain A: H.78, M.82, Y.441, E.444 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.13: 2 residues within 4Å: Chain A: R.243, V.289 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: G.117, E.198 Ligand excluded by PLIP

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

NAG.15: 1 residues within 4Å: Chain A: N.18 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.5 NAG.16: 2 residues within 4Å: Chain A: R.15, N.58 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.58 NAG.17: 2 residues within 4Å: Chain A: N.107, N.189 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.189 NAG.18: 5 residues within 4Å: Chain A: G.337, F.338, S.339, N.342, I.345 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.337 NAG.19: 3 residues within 4Å: Chain A: Y.478, N.482, E.483 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.482

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kosak, U. et al., Development of an in-vivo active reversible butyrylcholinesterase inhibitor. Sci Rep (2016)

Release Date

2017-01-18

Peptides

Cholinesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Cholinesterase

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