SMTL ID : 8cgo.1

Structure of human butyrylcholinesterase in complex with N-{[2-(benzyloxy)-3-methoxyphenyl]methyl}-N-[3-(2-fluorophenyl)propyl]cyclobutanamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

2 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.188, A:S.191, A:R.219, A:K.476, A:N.188 Water bridges: A:T.108, A:T.108

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.3: 6 residues within 4Å: Chain A: N.241, N.245, L.249, F.278, V.280, P.281 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.249 NAG-NAG-FUC.4: 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:S.338, A:G.336

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

NAG.5: 1 residues within 4Å: Chain A: N.256 No protein-ligand interaction detected (PLIP) 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:A.516 Salt bridges: A:K.323, A:R.515

1 x XB8: ~{N}-[3-(2-fluorophenyl)propyl]-~{N}-[(3-methoxy-2-phenylmethoxy-phenyl)methyl]cyclobutanamine(Non-covalent)

XB8.8: 16 residues within 4Å: Chain A: W.82, G.116, G.117, E.197, S.198, W.231, P.285, L.286, S.287, V.288, A.328, F.329, Y.332, F.398, W.430, H.438 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.82, A:V.288, A:A.328, A:F.329, A:Y.332, A:Y.332, A:H.438 Water bridges: A:G.116, A:G.117 Halogen bonds: A:Y.332

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

SIA.9: 3 residues within 4Å: Chain A: K.60, N.63, D.87 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.87 Hydrogen bonds: A:N.63 Water bridges: A:N.63, A:D.87 Salt bridges: A:K.60

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: L.18, L.29, Y.61, W.98, D.129, K.131 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.98, A:D.129, A:K.131

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

SO4.11: 5 residues within 4Å: Chain A: W.231, R.242, L.286, S.287, V.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.286, A:V.288 Salt bridges: A:R.242 SO4.12: 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 SO4.13: 4 residues within 4Å: Chain A: R.470, S.487, T.488, T.508 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 Water bridges: A:S.466 SO4.14: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pidany, F. et al., Highly selective butyrylcholinesterase inhibitors related to Amaryllidaceae alkaloids - Design, synthesis, and biological evaluation. Eur.J.Med.Chem. (2023)

Release Date

2023-06-14

Peptides

Cholinesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cholinesterase

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