SMTL ID : 7qhe.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 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: 4 residues within 4Å: Chain A: P.335, G.336, S.338, N.341 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.2: 7 residues within 4Å: Chain A: Y.237, N.241, N.245, K.248, L.249, F.278, P.281 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.248, A:L.249 Hydrogen bonds: A:K.248, A:F.278

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

NAG.3: 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.4: 3 residues within 4Å: Chain A: N.106, N.188, K.190 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.106 Hydrogen bonds: A:N.188 NAG.5: 3 residues within 4Å: Chain A: N.256, T.258, E.259 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.259 NAG.6: 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:R.465, 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

1 x C4I: (3~{S})-1-[[4-(naphthalen-1-ylcarbamoyl)phenyl]methyl]-~{N}-[3-(1,2,3,4-tetrahydroacridin-9-ylamino)propyl]piperidine-3-carboxamide(Non-covalent)

C4I.8: 24 residues within 4Å: Chain A: N.68, I.69, D.70, W.82, G.116, G.117, Q.119, T.120, E.197, W.231, T.284, P.285, L.286, S.287, A.328, F.329, Y.332, N.397, F.398, W.430, M.437, H.438, G.439, Y.440 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:N.68, A:W.82, A:W.82, A:Q.119, A:Q.119, A:T.120, A:W.231, A:W.231, A:L.286, A:L.286, A:A.328, A:Y.332, A:N.397, A:F.398, A:W.430, A:Y.440 Hydrogen bonds: A:L.286 Water bridges: A:N.68 pi-Stacking: A:W.82, A:W.82, A:F.329

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: W.231, 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

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

SO4.10: 4 residues within 4Å: Chain A: R.470, S.487, T.488, T.508 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.470, A:T.488, A:T.488, A:T.488, A:T.508 Water bridges: A:S.466, A:S.487, A:S.487, A:N.504, A:T.508 SO4.11: 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 SO4.12: 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

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

CL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: Y.385 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: T.512, K.513 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: K.513, R.520 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain A: K.499, I.510 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain A: N.85 Ligand excluded by PLIP CL.19: 1 residues within 4Å: Chain A: L.286 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

Related Entries With Identical Sequence