SMTL ID : 9r3b.1

Recombinant human Butyrylcholinesterase in complex with N-([(3R)-1-benzylpiperidin-3-yl]methyl)-N-(2-methoxyethyl)naphthalene-2-sulfonamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

2 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 2 residues within 4Å: Chain A: R.14, N.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.14, A:N.57 NAG-FUC.5: 4 residues within 4Å: Chain A: R.465, K.469, E.482, N.485 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.469, A:E.482 Hydrogen bonds: A:R.465, A:N.485

3 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: 6 residues within 4Å: Chain A: N.106, N.188, K.190, S.191, R.219, K.476 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.188, A:S.191, A:S.191, A:R.219, A:K.190 Water bridges: A:T.108, A:T.108 NAG-NAG-FUC.3: 6 residues within 4Å: Chain A: Y.237, N.241, N.245, K.248, L.249, F.278 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.245, A:K.248, A:L.249 Hydrogen bonds: A:F.278 NAG-NAG-FUC.4: 5 residues within 4Å: Chain A: P.335, G.336, S.338, N.341, N.342 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.336

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

NAG.6: 1 residues within 4Å: Chain A: N.256 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.256

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: T.234, R.242, S.287, V.288 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.234, A:R.242, A:R.242, A:L.286, A:V.288 GOL.10: 2 residues within 4Å: Chain A: T.512, K.513 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.512

1 x 01: N-(2-methoxyethyl)-N-[[(3R)-1-(phenylmethyl)piperidin-3-yl]methyl]naphthalene-2-sulfonamide

01.8: 22 residues within 4Å: Chain A: N.68, I.69, D.70, W.82, G.116, G.117, Q.119, T.120, S.198, W.231, L.286, S.287, V.288, A.328, F.329, Y.332, F.398, W.430, M.437, H.438, Y.440 Ligands: DMS.9 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.231, A:W.231, A:L.286, A:L.286, A:V.288, A:A.328, A:F.329, A:F.398, A:W.430, A:Y.440 Salt bridges: A:D.70 pi-Stacking: A:W.82, A:F.329

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

DMS.9: 7 residues within 4Å: Chain A: W.82, G.115, G.116, Y.128, E.197, S.198 Ligands: 01.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.198 Water bridges: A:G.116 Salt bridges: A:E.197

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.11: 6 residues within 4Å: Chain A: K.323, Y.420, K.513, L.514, R.515, Q.518 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.420, A:R.515, A:R.515 Water bridges: A:Y.500 Salt bridges: A:K.323, A:R.515

1 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.12: 3 residues within 4Å: Chain A: K.60, N.63, D.87 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.87 Water bridges: A:N.63, A:N.63, A:D.87, A:D.87 Salt bridges: A:K.60

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

SO4.13: 4 residues within 4Å: Chain A: Q.486, S.487, T.488, T.508 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.470, A:T.488, A:T.488, A:T.488 Water bridges: A:S.466, A:T.508, A:T.508 SO4.14: 2 residues within 4Å: Chain A: R.347, Q.351 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.351 Salt bridges: A:R.347 SO4.15: 4 residues within 4Å: Chain A: Q.316, G.413, N.414, N.415 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.316, A:N.414, A:N.415 Water bridges: A:N.415 SO4.16: 2 residues within 4Å: Chain A: N.85, H.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.85 Water bridges: A:H.126

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

CL.17: 3 residues within 4Å: Chain A: S.215, F.217, T.218 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kosak, U. et al., Chiral switch of a butyrylcholinesterase inhibitor for the treatment of Alzheimer's disease. Chem.Biol.Interact. (2025)

Release Date

2025-07-30

Peptides

Cholinesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cholinesterase

Related Entries With Identical Sequence