SMTL ID : 7qhd.1

Human Butyrylcholinesterase in complex with (S)-1-(4-((2-(1H-indol-3-yl)ethyl)carbamoyl)benzyl)-N-(3-((1,2,3,4-tetrahydroacridin-9-yl)amino)propyl)piperidine-3-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.14, A:N.57

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: 4 residues within 4Å: Chain A: N.106, N.188, K.190, S.191 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.188 Water bridges: A:T.108, A:K.476 NAG-NAG-FUC.3: 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:G.336

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

NAG.4: 1 residues within 4Å: Chain A: N.256 No protein-ligand interaction detected (PLIP) NAG.5: 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 NAG.6: 3 residues within 4Å: Chain A: N.241, L.244, N.245 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.244 Hydrogen bonds: A:N.241, A:N.245, A:N.245

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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.515, A:R.515, A:A.516 Water bridges: A:Y.500 Salt bridges: A:K.323, A:R.515

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: P.230, W.231, V.233, T.234, E.238, R.242, V.288 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.234, A:E.238, A:R.242, A:R.242, A:V.288 Water bridges: A:V.288 GOL.11: 2 residues within 4Å: Chain A: N.85, H.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.85 Water bridges: A:H.126 GOL.12: 3 residues within 4Å: Chain A: N.342, R.386, W.433 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.342, A:R.386, A:R.386, A:W.433 GOL.13: 7 residues within 4Å: Chain A: H.77, M.81, S.425, K.427, Y.440, E.443, Y.456 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.425, A:S.425 GOL.14: 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

1 x C0I: (3~{S})-1-[[4-[2-(1~{H}-indol-3-yl)ethylcarbamoyl]phenyl]methyl]-~{N}-[3-(1,2,3,4-tetrahydroacridin-9-ylamino)propyl]piperidine-3-carboxamide(Non-covalent)

C0I.9: 30 residues within 4Å: Chain A: N.68, I.69, D.70, W.82, G.115, G.116, G.117, Q.119, T.120, E.197, S.198, W.231, T.284, P.285, L.286, S.287, V.288, A.328, F.329, Y.332, F.357, V.393, N.397, F.398, W.430, M.437, H.438, G.439, Y.440 Ligands: SO4.15 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:W.82, A:Q.119, A:Q.119, A:T.120, A:W.231, A:L.286, A:L.286, A:A.328, A:F.329, A:Y.332, A:F.357, A:V.393, A:N.397, A:F.398, A:W.430, A:Y.440 Hydrogen bonds: A:T.284, A:P.285 Water bridges: A:D.70, A:G.116, A:G.117 pi-Stacking: A:W.82, A:W.82, A:F.329

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

SIA.10: 3 residues within 4Å: Chain A: K.60, N.63, D.87 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.87, A:D.87, A:S.89 Salt bridges: A:K.60

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

SO4.15: 4 residues within 4Å: Chain A: P.285, L.286, S.287 Ligands: C0I.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.286, A:S.287 Water bridges: A:A.277 SO4.16: 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 SO4.17: 6 residues within 4Å: Chain A: R.470, Q.486, S.487, T.488, T.508 Ligands: CL.25 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.470, A:T.488, A:T.488, A:T.508, A:T.508, A:T.508 Water bridges: A:S.466, A:S.466, A:S.466, A:Q.486, A:S.487 SO4.18: 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

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

CL.19: 2 residues within 4Å: Chain A: W.376, Y.385 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain A: G.39, R.40 Ligand excluded by PLIP CL.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain A: T.512 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain A: K.513, R.520 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain A: R.42, K.267 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain A: L.463 Ligands: SO4.17 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jing, L. et al., Rapid discovery and crystallography study of highly potent and selective butylcholinesterase inhibitors based on oxime-containing libraries and conformational restriction strategies. Bioorg.Chem. (2023)

Release Date

2022-12-21

Peptides

Cholinesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cholinesterase

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