SMTL ID : 9i5p.1

Recombinant human butyrylcholinesterase in complex with 1-(isobutylmethyl)-5-(2,4-difluorobenzyl)-N-(2-(dimethylamino)ethyl)-1H-indazole-6-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 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:N.188 Hydrophobic interactions: A:N.106 NAG-FUC.3: 7 residues within 4Å: Chain A: Y.237, N.241, N.245, K.248, L.249, F.278, P.281 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.278, A:Y.237, A:N.245 Hydrophobic interactions: A:P.281

1 x NAG- NAG- BMA- FUC: 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-FUC.4: 6 residues within 4Å: Chain A: P.335, G.336, F.337, S.338, N.341, N.342 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.336

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.5: 4 residues within 4Å: Chain A: R.452, R.465, E.482, N.485 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.452, A:R.452

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 01: 5-[(2,4-difluorophenyl)methyl]-N-[2-(dimethylamino)ethyl]-1-(2-methylpropyl)-1H-indazole-6-carboxamide

01.7: 18 residues within 4Å: Chain A: N.68, I.69, D.70, G.78, W.82, G.115, G.116, T.120, E.197, P.285, A.328, F.329, Y.332, W.430, M.437, H.438, G.439, Y.440 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:D.70, A:T.120, A:F.329, A:F.329, A:Y.332, A:Y.332, A:W.430 Salt bridges: A:E.197 pi-Cation interactions: A:W.82 Halogen bonds: A:Y.440

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

SIA.8: 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 Hydrogen bonds: A:N.63, A:D.87 Water bridges: A:K.60, A:K.60 Salt bridges: A:K.60

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 8 residues within 4Å: Chain A: P.230, W.231, V.233, T.234, R.242, L.286, S.287, V.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.233, A:R.242, A:V.288

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

MES.10: 5 residues within 4Å: Chain A: K.323, Y.420, R.515, A.516, Q.518 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.323, A:R.515, A:A.516 Salt bridges: A:K.323, A:R.515

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

SO4.11: 5 residues within 4Å: Chain A: R.470, Q.486, S.487, T.488, T.508 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.470, A:Q.486, A:T.488, A:T.488, A:T.508, A:T.508 SO4.12: 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 SO4.13: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferjancic Benetik, S. et al., Targeting Neuroinflammation and Cognitive Decline: First-in-Class Dual Butyrylcholinesterase and p38 alpha Mitogen-Activated Protein Kinase Inhibitors. J.Med.Chem. (2025)

Release Date

2025-08-20

Peptides

Cholinesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cholinesterase

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