SMTL ID : 6qad.1

Human Butyrylcholinesterase in complex with ((S)-2-(butylamino)-N-(2-(4-(dimethylamino)cyclohexyl)ethyl)-3-(1H-indol-3-yl)propanamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 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.42, N.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.42, A:N.85

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: 5 residues within 4Å: Chain A: P.363, G.364, S.366, N.369, N.370 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.363 NAG-NAG-FUC.3: 5 residues within 4Å: Chain A: Y.265, N.269, L.272, N.273, P.309 No protein-ligand interaction detected (PLIP)

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

NAG.4: 3 residues within 4Å: Chain A: N.134, N.216, K.218 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.216, A:K.218 NAG.5: 1 residues within 4Å: Chain A: N.284 No protein-ligand interaction detected (PLIP) NAG.6: 4 residues within 4Å: Chain A: R.493, K.497, E.510, N.513 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.497, A:E.510 Hydrogen bonds: A:R.493, A:N.513

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 8 residues within 4Å: Chain A: W.110, G.143, G.144, Y.156, E.225, S.226, H.466, G.467 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.226 Water bridges: A:G.144 Salt bridges: A:E.225 pi-Cation interactions: A:W.110

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 9 residues within 4Å: Chain A: H.105, M.109, S.453, K.455, L.456, P.457, Y.468, E.471, Y.484 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.105, A:S.453, A:S.453 GOL.9: 7 residues within 4Å: Chain A: M.44, L.46, L.57, Y.89, W.126, D.157, K.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.126, A:K.159, A:K.159 GOL.10: 5 residues within 4Å: Chain A: W.259, R.270, L.314, S.315, V.316 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.270, A:R.270, A:V.316 GOL.11: 3 residues within 4Å: Chain A: P.519, V.520, K.527 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.520, A:K.527

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

MES.12: 5 residues within 4Å: Chain A: K.351, Y.448, L.542, R.543, Q.546 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.543, A:Q.546 Salt bridges: A:K.351, A:R.543

1 x HUZ: (2~{S})-2-(butylamino)-~{N}-[2-[4-(dimethylamino)cyclohexyl]ethyl]-3-(1~{H}-indol-3-yl)propanamide(Non-covalent)

HUZ.13: 12 residues within 4Å: Chain A: G.144, G.145, Q.147, G.311, T.312, P.313, L.314, S.315, N.317, A.356, F.357, Y.360 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.147, A:F.357, A:F.357, A:Y.360, A:Y.360 Hydrogen bonds: A:P.313, A:S.315

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

SO4.14: 4 residues within 4Å: Chain A: Q.344, G.441, N.442, N.443 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.344, A:N.442, A:N.443 SO4.15: 5 residues within 4Å: Chain A: R.498, Q.514, S.515, T.516, T.536 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.498, A:Q.514, A:T.516, A:T.516, A:T.536, A:T.536 Water bridges: A:S.494, A:T.536 SO4.16: 2 residues within 4Å: Chain A: R.375, Q.379 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.379 Salt bridges: A:R.375 SO4.17: 3 residues within 4Å: Chain A: R.548, F.549, F.553 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meden, A. et al., Tryptophan-derived butyrylcholinesterase inhibitors as promising leads against Alzheimer's disease. Chem.Commun.(Camb.) (2019)

Release Date

2019-03-27

Peptides

Cholinesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cholinesterase

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