SMTL ID : 5dyw.1 (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: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: I.5, N.18, T.25, A.102 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: K.106, N.107, N.189, K.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.191, A:K.191 NAG-NAG.5: 6 residues within 4Å: Chain A: Y.478, N.480, N.482, E.483, T.484, Q.485 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-FUC.2: 3 residues within 4Å: Chain A: R.15, I.56, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.4: 6 residues within 4Å: Chain A: N.242, N.246, K.249, F.279, V.281, P.282 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.282, A:K.249 Hydrogen bonds: A:F.279, A:V.281

1 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.6: 6 residues within 4Å: Chain A: E.483, N.487, S.488, T.489, E.507, T.509 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.487, A:T.489, A:T.489

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

5HF.7: 19 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, F.399, W.431, M.438, H.439, Y.441 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.232, A:L.287, A:A.329, A:F.330, A:F.399, A:W.431, A:Y.441 Hydrogen bonds: A:T.121 Water bridges: A:N.69 pi-Stacking: A:F.330

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: L.19, Y.62, W.99, D.130, K.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.99, A:D.130, A:K.132 GOL.9: 7 residues within 4Å: Chain A: Q.180, P.190, K.191, S.216, F.218, T.219, K.314 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.180, A:P.190, A:K.314 GOL.10: 5 residues within 4Å: Chain A: Y.397, C.401, P.402, W.523, T.524 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.229, A:C.401 GOL.11: 7 residues within 4Å: Chain A: N.11, Y.34, S.49, L.50, Q.177, W.178, K.181 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.50, A:L.50 Water bridges: A:N.11

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

EDO.12: 2 residues within 4Å: Chain A: N.480, W.491 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.480 EDO.13: 3 residues within 4Å: Chain A: T.109, N.189, K.477 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.189 EDO.14: 4 residues within 4Å: Chain A: H.78, K.428, Y.441, E.444 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.78, A:E.444 EDO.15: 3 residues within 4Å: Chain A: K.495, S.496, T.497 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.496, A:S.496, A:T.497, A:T.497 EDO.16: 7 residues within 4Å: Chain A: D.325, R.387, E.388, E.433, W.434, G.436 Ligands: CL.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.387, A:E.388, A:E.388 EDO.17: 7 residues within 4Å: Chain A: L.30, G.31, W.57, N.58, K.61, A.63, Y.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.58, A:K.61 Water bridges: A:Y.95

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

CL.18: 2 residues within 4Å: Chain A: R.387 Ligands: EDO.16 Ligand excluded by PLIP CL.19: 1 residues within 4Å: Chain A: E.198 Ligand excluded by PLIP

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.20: 3 residues within 4Å: Chain A: S.427, N.456, Y.457 No protein-ligand interaction detected (PLIP)

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

NAG.21: 2 residues within 4Å: Chain A: S.339, N.342 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.342 Water bridges: A:G.337, A:G.337

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
A

Cholinesterase

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