SMTL ID : 4xii.1

X-ray structure of human butyrylcholinesterase in complex with N-((1-(2,3-dihydro-1H-inden-2-yl)piperidin-3-yl)methyl)-8-hydroxy-N-(2-methoxyethyl)-5-nitroquinoline-7-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

1 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.1: 4 residues within 4Å: Chain A: R.14, D.54, I.55, N.57 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 3 residues within 4Å: Chain A: N.106, N.188, K.190 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: E.238, N.241, N.245 Ligands: FUL.8 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: Y.477, N.479, N.481, E.482, T.483, Q.484 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.477 NAG-NAG.5: 2 residues within 4Å: Chain A: N.486 Ligands: FUL.11 No protein-ligand interaction detected (PLIP)

2 x 40V: N-{[(3R)-1-(2,3-dihydro-1H-inden-2-yl)piperidin-3-yl]methyl}-8-hydroxy-N-(2-methoxyethyl)-5-nitroquinoline-7-carboxamide(Non-covalent)

40V.6: 18 residues within 4Å: Chain A: N.68, I.69, D.70, W.82, G.116, G.117, T.120, E.197, S.198, W.231, P.285, L.286, S.287, F.329, Y.332, F.398, H.438, G.439 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:N.68, A:D.70, A:T.120, A:L.286, A:F.329, A:F.329, A:Y.332, A:Y.332 Hydrogen bonds: A:T.120, A:S.198 Water bridges: A:G.116 Salt bridges: A:D.70 pi-Stacking: A:W.231, A:W.231, A:F.329 40V.17: 21 residues within 4Å: Chain B: N.68, I.69, D.70, W.82, G.116, G.117, Q.119, T.120, E.197, S.198, W.231, P.285, L.286, S.287, V.288, F.329, Y.332, F.398, H.438, G.439 Ligands: EDO.29 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:D.70, B:T.120, B:V.288, B:F.329, B:F.329, B:Y.332, B:Y.332 Hydrogen bonds: B:S.198 Salt bridges: B:D.70 pi-Stacking: B:W.231, B:W.231, B:F.329 pi-Cation interactions: B:Y.332

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

NAG.7: 1 residues within 4Å: Chain A: N.17 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.17 Hydrogen bonds: A:N.17 NAG.9: 5 residues within 4Å: Chain A: G.336, S.338, N.341, I.344 Ligands: FUC.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.336, A:S.338 NAG.18: 3 residues within 4Å: Chain B: I.4, N.17, T.24 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.4, B:I.4, B:T.24, B:T.24 NAG.19: 3 residues within 4Å: Chain B: R.14, I.55, N.57 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.14 NAG.20: 3 residues within 4Å: Chain B: N.106, N.188, K.190 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.188, B:N.188, B:K.190 NAG.21: 5 residues within 4Å: Chain B: Y.237, N.241, N.245, P.281 Ligands: FUL.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.245 NAG.23: 2 residues within 4Å: Chain B: N.256, E.259 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.256 NAG.24: 6 residues within 4Å: Chain B: G.336, S.338, N.341, N.342, S.343, I.344 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.336 Water bridges: B:G.336 NAG.25: 4 residues within 4Å: Chain B: K.427, R.453, D.454, N.455 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.427, B:R.453, B:N.455 NAG.26: 4 residues within 4Å: Chain B: N.473, N.481, E.482, T.483 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.473, B:N.479

3 x FUL: beta-L-fucopyranose(Non-covalent)

FUL.8: 5 residues within 4Å: Chain A: N.245, F.278, P.281 Ligands: NAG-NAG.3, NAG-NAG.3 No protein-ligand interaction detected (PLIP) FUL.11: 8 residues within 4Å: Chain A: S.466, E.482, N.486, S.487, T.488, T.508 Ligands: NAG-NAG.5, NAG-NAG.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.486, A:T.488, A:T.488 FUL.22: 5 residues within 4Å: Chain B: N.245, L.249, F.278, P.281 Ligands: NAG.21 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.281 Hydrogen bonds: B:N.245

1 x FUC: alpha-L-fucopyranose(Non-functional Binders)

FUC.10: 1 residues within 4Å: Ligands: NAG.9 No protein-ligand interaction detected (PLIP)

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

CL.12: 2 residues within 4Å: Chain A: F.21, R.465 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain A: R.470, N.481, T.488, S.489, W.490 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: R.386 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain B: T.234, R.242, V.288 Ligand excluded by PLIP

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

EDO.15: 3 residues within 4Å: Chain A: R.386, E.387, W.433 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.386, A:E.387 EDO.16: 5 residues within 4Å: Chain A: P.104, K.105, N.106, A.107, R.138 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.105, A:N.106, A:N.106, A:R.138 EDO.28: 4 residues within 4Å: Chain B: N.266, K.267, D.268, E.271 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.268, B:D.268, B:D.268 EDO.29: 3 residues within 4Å: Chain B: N.68, Q.119 Ligands: 40V.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.68, B:N.289 Water bridges: B:E.276, B:P.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knez, D. et al., Structure-based development of nitroxoline derivatives as potential multifunctional anti-Alzheimer agents. Bioorg.Med.Chem. (2015)

Release Date

2015-07-08

Peptides

Cholinesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cholinesterase