SMTL ID : 6f7q.1

Human Butyrylcholinesterase complexed with N-Propargyliperidines

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

1 x NAG- FUL: beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUL.1: 4 residues within 4Å: Chain A: R.14, D.54, I.55, N.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.55, A:N.57

3 x NAG- NAG- FUL: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUL.2: 6 residues within 4Å: Chain A: N.241, N.245, L.249, F.278, V.279, P.281 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.245 NAG-NAG-FUL.3: 2 residues within 4Å: Chain A: N.341, N.342 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.341 NAG-NAG-FUL.6: 7 residues within 4Å: Chain B: N.241, N.245, K.248, L.249, F.278, V.279, P.281 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.245, B:K.248

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 3 residues within 4Å: Chain B: N.106, N.188, K.190 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.190, B:K.190

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.5: 2 residues within 4Å: Chain B: S.338, N.341 No protein-ligand interaction detected (PLIP)

4 x CWQ: 2-[[(3~{R})-1-(2,3-dihydro-1~{H}-inden-2-yl)piperidin-3-yl]methyl-(8-oxidanylquinolin-2-yl)carbonyl-amino]ethyl-dimethyl-azanium(Non-covalent)

CWQ.7: 16 residues within 4Å: Chain A: H.372, Y.373, D.375, V.377, Q.517, Q.518 Chain B: I.462, L.463, S.466, N.485, N.486, N.504, E.506, S.507, T.508 Ligands: EDO.23 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:H.372, A:V.377, A:Q.517, A:Q.518, B:I.462, B:L.463, B:T.508 Water bridges: A:Q.518 Salt bridges: A:D.375 pi-Stacking: A:Y.373 Hydrogen bonds: B:T.508 CWQ.8: 17 residues within 4Å: Chain A: I.69, D.70, W.82, G.116, G.117, T.120, E.197, S.198, W.231, P.285, L.286, V.288, A.328, F.329, Y.332, F.398, H.438 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:D.70, A:T.120, A:V.288, A:F.329, A:F.329, A:Y.332, A:F.398 Hydrogen bonds: A:H.438 Salt bridges: A:D.70, A:E.197 pi-Stacking: A:W.231, A:W.231, A:F.329 CWQ.20: 16 residues within 4Å: Chain A: I.462, L.463, S.466, N.485, N.486, N.504, E.506, S.507, T.508 Chain B: H.372, Y.373, D.375, V.377, Q.517, Q.518 Ligands: EDO.14 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:H.372, B:V.377, B:Q.517, B:Q.518, A:I.462, A:L.463, A:T.508 Salt bridges: B:D.375 pi-Stacking: B:Y.373 Hydrogen bonds: A:T.508 CWQ.21: 17 residues within 4Å: Chain B: N.68, I.69, D.70, W.82, G.116, G.117, T.120, E.197, S.198, W.231, L.286, S.287, V.288, A.328, F.329, Y.332, H.438 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:D.70, B:T.120, B:V.288, B:A.328, B:F.329, B:Y.332 Hydrogen bonds: B:T.120, B:H.438 Salt bridges: B:D.70, B:E.197 pi-Stacking: B:W.231, B:W.231, B:F.329 pi-Cation interactions: B:Y.332

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 1 residues within 4Å: Chain A: R.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.135, A:R.135 GOL.10: 3 residues within 4Å: Chain A: K.513, A.516, R.520 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.513 GOL.11: 6 residues within 4Å: Chain A: P.189, K.190, S.215, F.217, T.218, K.313 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.190, A:S.215, A:K.313, A:K.313

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.12: 4 residues within 4Å: Chain A: H.77, M.81, E.443, Y.456 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.456 Water bridges: A:K.427 EDO.13: 6 residues within 4Å: Chain A: L.18, L.29, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.98, A:K.131 EDO.14: 7 residues within 4Å: Chain A: S.466, R.470, S.487, T.488, L.503, T.508 Ligands: CWQ.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.466, A:R.470, A:T.488, A:T.508 EDO.23: 6 residues within 4Å: Chain B: S.466, R.470, S.487, T.488, T.508 Ligands: CWQ.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.466, B:R.470, B:T.488

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

NAG.15: 3 residues within 4Å: Chain A: N.106, N.188, K.190 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.106 Hydrogen bonds: A:N.188 Water bridges: A:K.190 NAG.16: 4 residues within 4Å: Chain A: R.465, K.469, E.482, N.485 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.469 Hydrogen bonds: A:N.485 NAG.24: 2 residues within 4Å: Chain B: R.14, N.57 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.14, B:N.57 NAG.25: 4 residues within 4Å: Chain B: R.465, K.469, E.482, N.485 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.465, B:N.485

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

SO4.17: 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 SO4.18: 4 residues within 4Å: Chain A: A.62, N.63, D.91, Y.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.63, A:D.91 SO4.19: 7 residues within 4Å: Chain A: P.230, W.231, V.233, T.234, E.238, R.242, V.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.288, A:V.288 Salt bridges: A:R.242 SO4.26: 6 residues within 4Å: Chain B: P.230, W.231, T.234, E.238, R.242, V.288 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.233 Salt bridges: B:R.242 SO4.27: 4 residues within 4Å: Chain B: Q.316, G.413, N.414, N.415 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.316, B:G.413, B:N.414, B:N.415

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

CL.22: 1 residues within 4Å: Chain B: R.515 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knez, D. et al., Multi-target-directed ligands for treating Alzheimer's disease: Butyrylcholinesterase inhibitors displaying antioxidant and neuroprotective activities. Eur.J.Med.Chem. (2018)

Release Date

2018-09-05

Peptides

Cholinesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cholinesterase

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