SMTL ID : 7bo3.1

Human Butyrylcholinesterase in complex with N-(2-(1H-Indol-3-yl)ethyl)-2-cycloheptyl-N-methylethan-1-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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.3: 7 residues within 4Å: Chain A: Y.237, N.241, N.245, L.249, F.278, V.280, P.281 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.245, A:L.249, A:Y.237 Hydrogen bonds: A:F.278, A:N.245

1 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: 5 residues within 4Å: Chain A: P.335, G.336, S.338, N.341, N.342 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.335

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

NAG.4: 2 residues within 4Å: Chain A: N.106, N.188 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.188 NAG.5: 2 residues within 4Å: Chain A: N.256, E.259 No protein-ligand interaction detected (PLIP) NAG.6: 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

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

MES.7: 5 residues within 4Å: Chain A: K.323, Y.420, L.514, R.515, Q.518 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.515, A:R.515 Salt bridges: A:K.323, A:R.515

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:G.413, A:N.414, A:N.415 SO4.9: 4 residues within 4Å: Chain A: R.470, S.487, T.488, T.508 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.470, A:T.488, A:T.488, A:T.488, A:T.508 SO4.10: 2 residues within 4Å: Chain A: R.347, Q.351 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.351, A:Q.351 Salt bridges: A:R.347 SO4.15: 5 residues within 4Å: Chain A: W.231, R.242, L.286, 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

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 5 residues within 4Å: Chain A: L.18, Y.61, W.98, D.129, K.131 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.98, A:K.131 Water bridges: A:D.129 GOL.12: 9 residues within 4Å: Chain A: W.82, G.115, G.116, G.117, Y.128, E.197, S.198, H.438 Ligands: IA4.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.116, A:G.117, A:E.197, A:S.198 Water bridges: A:W.82

1 x IA4: ~{N}-(2-cycloheptylethyl)-2-(1~{H}-indol-3-yl)-~{N}-methyl-ethanamine(Non-covalent)

IA4.13: 14 residues within 4Å: Chain A: W.82, G.117, S.198, W.231, P.285, L.286, S.287, V.288, F.329, Y.332, F.398, W.430, H.438 Ligands: GOL.12 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.288, A:F.329, A:Y.332, A:F.398, A:W.430 Hydrogen bonds: A:S.287 pi-Stacking: A:W.231, A:W.231

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

SIA.14: 6 residues within 4Å: Chain A: F.76, K.339, D.340, P.429, W.430, P.431 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.339, A:D.340, A:D.340

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meden, A. et al., From tryptophan-based amides to tertiary amines: Optimization of a butyrylcholinesterase inhibitor series. Eur.J.Med.Chem. (2022)

Release Date

2022-03-02

Peptides

Cholinesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cholinesterase

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