SMTL ID : 7zpb.1

Structure of hemiacetylated human butyrylcholinesterase upon reaction with 8-(3-(4-(prop-2-yn-1-yl)piperazin-1-yl)propoxy)quinoline-2-carbaldehyde

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

monomer

Ligands

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.1: 2 residues within 4Å: Chain A: R.14, N.57 No protein-ligand interaction detected (PLIP) 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:G.336

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

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:K.190, A:R.219, A:N.188 NAG-FUC.3: 8 residues within 4Å: Chain A: Y.237, N.241, N.245, K.248, L.249, F.278, V.280, P.281 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.245, A:L.249, A:Y.237 Hydrogen bonds: A:K.248, A:Y.237, A:N.245 NAG-FUC.5: 4 residues within 4Å: Chain A: R.465, K.469, E.482, N.485 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: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 1 residues within 4Å: Chain A: N.256 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 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 GOL.8: 2 residues within 4Å: Chain A: E.411, W.412 No protein-ligand interaction detected (PLIP) GOL.13: 8 residues within 4Å: Chain A: H.77, M.81, H.126, V.127, K.427, P.429, Y.440, E.443 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.443

1 x JS0: [8-[3-(4-prop-2-ynylpiperazin-1-yl)propoxy]quinolin-2-yl]methanol(Covalent)

JS0.9: 17 residues within 4Å: Chain A: W.82, G.115, G.116, G.117, Q.119, S.198, A.199, W.231, P.285, L.286, S.287, V.288, Y.332, W.430, H.438, Y.440 Ligands: PPI.12 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.286, A:V.288, A:Y.440 Hydrogen bonds: A:G.116, A:G.117, A:A.199 pi-Stacking: A:W.231, A:W.231, A:F.329, A:F.329

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

SIA.10: 3 residues within 4Å: Chain A: K.60, N.63, D.87 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.63 Water bridges: A:D.87 Salt bridges: A:K.60

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

MES.11: 6 residues within 4Å: Chain A: K.323, Y.420, Y.500, 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 PPI: PROPANOIC ACID(Non-covalent)

PPI.12: 6 residues within 4Å: Chain A: W.82, G.116, E.197, S.198, H.438 Ligands: JS0.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.82 Salt bridges: A:H.438

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

SO4.14: 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 SO4.15: 5 residues within 4Å: Chain A: R.470, Q.486, S.487, T.488, T.508 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.470, A:S.487, A:T.488, A:T.488, A:T.508 Water bridges: A:S.466, A:T.508, A:T.508 SO4.16: 4 residues within 4Å: Chain A: W.231, R.242, S.287, V.288 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.231, A:V.288 Water bridges: A:R.242, A:R.242 Salt bridges: A:R.242 SO4.17: 3 residues within 4Å: Chain A: R.520, F.521, F.525 No protein-ligand interaction detected (PLIP) SO4.18: 3 residues within 4Å: Chain A: R.347, K.348, Q.351 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.351 Salt bridges: A:R.347, A:K.348

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knez, D. et al., 8-Hydroxyquinolylnitrones as multifunctional ligands for the therapy of neurodegenerative diseases. Acta Pharm Sin B (2023)

Release Date

2023-02-01

Peptides

Cholinesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cholinesterase

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