SMTL ID : 8ai7.1

Structure of carbamoylated human butyrylcholinesterase upon reaction with 3-(((2-cycloheptylethyl)(methyl)amino)methyl)-1H-indol-7-yl N,N-dimethylcarbamate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.14, A:N.57 NAG-FUC.2: 6 residues within 4Å: Chain A: N.106, N.188, K.190, S.191, R.219, K.476 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.188, A:S.191, A:R.219, A:N.188 Water bridges: A:T.108, A:R.219, A:R.219, A:N.106 NAG-FUC.4: 5 residues within 4Å: Chain A: R.465, K.469, E.482, N.485 Ligands: CL.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.469, A:E.482 Hydrogen bonds: A:R.465, A:N.485

1 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.3: 5 residues within 4Å: Chain A: P.335, G.336, S.338, N.341, N.342 No protein-ligand interaction detected (PLIP)

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

SO4.5: 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.415 Water bridges: A:N.415 SO4.6: 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 SO4.7: 5 residues within 4Å: Chain A: S.487, T.488, S.507, T.508 Ligands: CL.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.470, A:T.488, A:T.488, A:T.508, A:T.508, A:T.508

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

CL.8: 2 residues within 4Å: Chain A: R.465 Ligands: NAG-FUC.4 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: T.512 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: L.463 Ligands: SO4.7 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain A: R.265 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain A: N.85 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: R.515 Ligands: NA.15 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: Y.420, R.515 Ligands: NA.15 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.15: 3 residues within 4Å: Chain A: R.515 Ligands: CL.13, CL.14 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.515

1 x M8X: 3-[[2-cycloheptylethyl(methyl)amino]methyl]-1~{H}-indol-7-ol(Non-covalent)

M8X.16: 7 residues within 4Å: Chain A: W.82, P.285, A.328, Y.332, W.430, M.437, H.438 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.328, A:Y.332, A:Y.332, A:Y.332, A:W.430

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

NAG.17: 2 residues within 4Å: Chain A: N.256, T.258 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.258 NAG.18: 5 residues within 4Å: Chain A: N.241, L.244, N.245, K.248 Ligands: GOL.21 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.244 Hydrogen bonds: A:N.245, A:K.248, A:K.248

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 6 residues within 4Å: Chain A: L.18, L.29, Y.61, W.98, D.129, K.131 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.98, A:K.131, A:K.131 Water bridges: A:D.129 GOL.20: 7 residues within 4Å: Chain A: M.81, S.425, K.427, L.428, Y.440, E.443, Y.456 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.425, A:S.425, A:K.427, A:K.427 GOL.21: 4 residues within 4Å: Chain A: N.245, K.248, F.278 Ligands: NAG.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.278 GOL.22: 7 residues within 4Å: Chain A: W.231, T.234, R.242, V.280, L.286, S.287, V.288 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.234, A:R.242, A:L.286, A:V.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meden, A. et al., Pseudo-irreversible butyrylcholinesterase inhibitors: Structure-activity relationships, computational and crystallographic study of the N-dialkyl O-arylcarbamate warhead. Eur.J.Med.Chem. (2023)

Release Date

2023-02-01

Peptides

Cholinesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

Cholinesterase