SMTL ID : 9r9d.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

monomer

Ligands

1 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

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: K.105, N.106, N.188, K.190, S.191, K.476 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.188, A:S.191, A:R.219, A:K.190 Water bridges: A:R.219, A:K.476 Hydrophobic interactions: A:K.190 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: 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:S.338

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

NAG.5: 1 residues within 4Å: Chain A: N.256 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.256 NAG.6: 4 residues within 4Å: Chain A: R.465, K.469, E.482, N.485 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.469 Hydrogen bonds: A:N.485

1 x 01: ~{N}-(2-methoxyethyl)-~{N}-[[(3~{R})-1-prop-2-ynylpyrrolidin-3-yl]methyl]naphthalene-2-carboxamide

01.7: 17 residues within 4Å: Chain A: W.82, G.116, G.117, T.120, E.197, S.198, W.231, P.285, L.286, S.287, V.288, A.328, F.329, Y.332, F.398, H.438, G.439 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.231, A:V.288, A:A.328, A:F.329, A:Y.332, A:F.398 pi-Stacking: A:W.231, A:W.231, A:F.329, A:F.329 pi-Cation interactions: A:Y.332

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

SO4.8: 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 SO4.9: 5 residues within 4Å: Chain A: W.231, E.238, R.242, S.287, V.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.231, A:V.288 Salt bridges: A:R.242 SO4.10: 5 residues within 4Å: Chain A: R.470, Q.486, S.487, T.488, T.508 10 PLIP interactions: 10 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.466, A:S.466, A:T.508, A:T.508 SO4.11: 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.12: 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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