SMTL ID : 9r9e.1

Recombinant human butyrylcholinesterase in complex with N-(3-methoxypropyl)-N-{[1-(prop-2-yn-1-yl)pyrrolidin-3-yl]methyl}naphthalene-2-sulfonamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

monomer

Ligands

3 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.14 NAG-FUC.2: 4 residues within 4Å: Chain A: N.106, N.188, K.190, S.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.188, A:S.191, A:N.188, A:K.190 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

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.3: 9 residues within 4Å: Chain A: Y.237, N.241, N.245, K.248, L.249, F.278, V.280, P.281, Y.282 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.245, A:L.249 Hydrogen bonds: A:K.248, A:F.278 NAG-NAG-FUC.4: 6 residues within 4Å: Chain A: P.335, G.336, S.338, D.340, N.341, N.342 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.340 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 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: L.18, L.29, Y.61, W.98, D.129, K.131 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.98, A:D.129, A:K.131

1 x 01: ~{N}-(3-methoxypropyl)-~{N}-[[(3~{S})-1-prop-2-ynylpyrrolidin-3-yl]methyl]naphthalene-2-sulfonamide

01.8: 15 residues within 4Å: Chain A: W.82, G.116, G.117, T.120, S.198, W.231, P.285, L.286, S.287, V.288, F.329, Y.332, F.398, W.430 Ligands: ACT.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.329, A:F.398, A:W.430 Salt bridges: A:D.70 pi-Stacking: A:W.231, A:W.231, A:F.329

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 4 residues within 4Å: Chain A: W.82, E.197, H.438 Ligands: 01.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.116

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

SO4.10: 4 residues within 4Å: Chain A: Q.316, G.413, N.414, N.415 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.316, A:N.414, A:N.415 SO4.11: 4 residues within 4Å: Chain A: R.470, 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, A:T.508 Water bridges: A:S.466, A:S.487 SO4.12: 4 residues within 4Å: Chain A: W.231, R.242, S.287, V.288 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.231, A:V.288 Water bridges: A:R.242, A:R.242 Salt bridges: A:R.242 SO4.13: 3 residues within 4Å: Chain A: K.323, Y.420, R.515 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.420 Salt bridges: A:K.323, A:R.515 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

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

CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kosak, U. et al., N-Propargylpyrrolidine-based butyrylcholinesterase and monoamine oxidase inhibitors. Chem.Biol.Interact. (2025)

Release Date

2025-08-13

Peptides

Cholinesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cholinesterase

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