SMTL ID : 9i03.1

Structure of recombinant human butyrylcholinesterase in complex with (R)-N-((1-benzylpyrrolidin-3-yl)methyl)-N-methylnaphthalene-2-sulfonamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

monomer

Ligands

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.1: 7 residues within 4Å: Chain A: Y.237, N.241, N.245, L.249, F.278, V.280, P.281 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.249 Hydrogen bonds: A:F.278, A:V.280 NAG-NAG-FUC.2: 4 residues within 4Å: Chain A: G.336, S.338, N.341, N.342 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.336

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

NAG-FUC.3: 4 residues within 4Å: Chain A: R.465, K.469, E.482, N.485 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.469, A:E.482 Hydrogen bonds: A:R.465, A:N.485 Water bridges: A:R.465

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.4: 2 residues within 4Å: Chain A: R.14, N.57 No protein-ligand interaction detected (PLIP)

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

NAG.5: 2 residues within 4Å: Chain A: N.106, N.188 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.188 NAG.6: 2 residues within 4Å: Chain A: N.256, T.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.256, A:T.258

3 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:Y.61, A:K.131, A:K.131 GOL.9: 2 residues within 4Å: Chain A: R.347, Q.351 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.347, A:R.347, A:Q.351 GOL.10: 8 residues within 4Å: Chain A: H.77, M.81, S.425, K.427, L.428, P.429, Y.440, E.443 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.425, A:S.425, A:E.443

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

MES.8: 6 residues within 4Å: Chain A: K.323, Y.420, Y.500, L.514, R.515, Q.518 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.515, A:R.515 Water bridges: A:D.324, A:Q.518 Salt bridges: A:K.323, A:R.515

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

SIA.11: 5 residues within 4Å: Chain A: 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 Water bridges: A:E.432

1 x 01: ~{N}-methyl-~{N}-[[(3~{R})-1-(phenylmethyl)pyrrolidin-3-yl]methyl]naphthalene-2-sulfonamide

01.12: 20 residues within 4Å: Chain A: 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: PPI.13 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:D.70, 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.231, A:W.231

1 x PPI: PROPANOIC ACID(Non-covalent)

PPI.13: 5 residues within 4Å: Chain A: W.82, E.197, S.198, H.438 Ligands: 01.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.198, A:S.198 Water bridges: A:G.116 Salt bridges: A:H.438

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

SO4.14: 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 SO4.15: 5 residues within 4Å: Chain A: R.470, Q.486, S.487, T.488, T.508 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.470, A:S.487, A:T.488, A:T.488, A:T.508, A:T.508 Water bridges: A:S.466 SO4.16: 4 residues within 4Å: Chain A: R.242, L.286, S.287, V.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.288, A:V.288 Salt bridges: A:R.242 SO4.17: 2 residues within 4Å: Chain A: N.85, H.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.85 Water bridges: A:H.126, A:H.126

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

CL.18: 1 residues within 4Å: Chain A: Y.385 Ligand excluded by PLIP CL.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kosak, U. et al., Lead Optimization of a Butyrylcholinesterase Inhibitor for the Treatment of Alzheimer's Disease. J.Med.Chem. (2025)

Release Date

2025-07-02

Peptides

Cholinesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cholinesterase

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