SMTL ID : 9i5q.1

Recombinant human butyrylcholinesterase in complex with 2-(cyclohexylmethyl)-5-(2,4-difluorophenoxy)-N-(2-(3-(methoxymethyl)piperidin-1-yl)ethyl)-2H-indazole-6-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 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: 5 residues within 4Å: Chain A: N.106, N.188, K.190, S.191, K.476 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.188, A:S.191, A:R.219, A:N.188, A:K.190 Hydrophobic interactions: A:N.106

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.2: 7 residues within 4Å: Chain A: Y.237, N.241, N.245, L.249, F.278, P.281, Y.282 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.245, A:Y.282 NAG-NAG-FUC.3: 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

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

NAG.4: 2 residues within 4Å: Chain A: R.14, N.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.57 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.469 Hydrogen bonds: A:R.465, A:N.485 Water bridges: A:N.485

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.131, A:K.131 GOL.10: 7 residues within 4Å: Chain A: I.462, L.463, S.466, N.504, T.505, T.508 Ligands: SO4.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.462, A:S.466, A:T.508 Water bridges: A:T.508, A:T.508 GOL.11: 7 residues within 4Å: Chain A: W.231, V.233, T.234, E.238, R.242, S.287, V.288 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.234, A:R.242, A:R.242, A:V.288 Water bridges: A:T.284

1 x 01: 5-[2,4-bis(fluoranyl)phenoxy]-2-(cyclohexylmethyl)-~{N}-[2-[(3~{R})-3-(methoxymethyl)piperidin-1-yl]ethyl]indazole-6-carboxamide

01.8: 20 residues within 4Å: Chain A: D.70, W.82, G.116, G.117, T.120, S.198, W.231, T.284, P.285, L.286, V.288, A.328, F.329, Y.332, F.357, V.393, N.397, F.398, H.438, Y.440 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:D.70, A:T.120, A:L.286, A:F.329, A:F.357, A:V.393, A:N.397, A:F.398, A:F.398, A:Y.440 Water bridges: A:T.120

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

MES.9: 5 residues within 4Å: Chain A: K.323, Y.420, L.514, R.515, Q.518 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.515, A:R.515, A:A.516, A:Q.518 Salt bridges: A:K.323, A:R.515

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

SO4.12: 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 SO4.13: 6 residues within 4Å: Chain A: R.470, Q.486, S.487, T.488, T.508 Ligands: GOL.10 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.470, A:Q.486, A:T.488, A:T.488, A:T.508, A:T.508 Water bridges: A:S.466 SO4.14: 2 residues within 4Å: Chain A: P.431, E.432 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.432 SO4.15: 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

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

CL.16: 2 residues within 4Å: Chain A: K.513, R.520 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain A: W.376, Y.385 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain A: C.66, Q.270 Ligand excluded by PLIP

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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