SMTL ID : 8aen.1

Human acetylcholinesterase in complex with zinc and N,N,N-trimethyl-2-oxo-2-(2-(pyridin-2-ylmethylene)hydrazineyl)ethan-1-aminium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

homo-dimer

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: 7 residues within 4Å: Chain A: A.343, P.344, G.345, F.346, S.347, N.350, L.353 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.347, A:G.345 NAG-NAG-FUC.4: 5 residues within 4Å: Chain B: A.343, P.344, G.345, S.347, N.350 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.344 Hydrogen bonds: B:G.345

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.2: 2 residues within 4Å: Chain A: N.265, T.267 No protein-ligand interaction detected (PLIP)

1 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-SIA.3: 9 residues within 4Å: Chain B: P.49, P.50, P.52, P.168, L.174, R.177, Q.181, P.217, D.306 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.181, B:P.217, B:Q.181, B:D.306 Salt bridges: B:R.177

2 x LWL: N,N,N-trimethyl-2-oxo-2-(2-(pyridin-2-ylmethylene)hydrazineyl)ethan-1-aminium(Non-covalent)

LWL.5: 12 residues within 4Å: Chain A: W.86, G.121, G.122, Y.124, E.202, S.203, W.236, V.294, Y.337, F.338, H.447 Ligands: ZN.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.236, A:V.294, A:F.338 Hydrogen bonds: A:G.122, A:Y.124 Water bridges: A:Y.337 Salt bridges: A:E.202 pi-Cation interactions: A:W.86, A:W.86 LWL.42: 12 residues within 4Å: Chain B: W.86, G.121, G.122, Y.124, E.202, S.203, W.236, V.294, Y.337, F.338, H.447 Ligands: ZN.43 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.236, B:V.294, B:F.338 Hydrogen bonds: B:Y.124 Salt bridges: B:E.202 pi-Cation interactions: B:W.86, B:W.86

4 x ZN: ZINC ION(Non-covalent)

ZN.6: 3 residues within 4Å: Chain A: S.203, H.447 Ligands: LWL.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.203, A:H.447 ZN.35: 3 residues within 4Å: Chain A: H.381 Chain B: H.381 Ligands: CL.63 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.381, B:H.381 ZN.36: 3 residues within 4Å: Chain A: H.287 Ligands: CL.23, CL.26 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.287, H2O.3 ZN.43: 3 residues within 4Å: Chain B: S.203, H.447 Ligands: LWL.42 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.203, B:H.447

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

SO4.7: 3 residues within 4Å: Chain A: Q.413, R.417, N.533 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: R.356, L.360 Chain B: R.534 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: T.504, G.506, A.507 Ligand excluded by PLIP SO4.10: 1 residues within 4Å: Chain A: H.322 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: G.240, M.241, G.242 Ligands: CL.32 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: F.80, K.348 Ligand excluded by PLIP SO4.13: 1 residues within 4Å: Chain A: R.90 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain A: P.108, T.109, S.110, R.143 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain A: V.520, R.521, R.522 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain A: N.317, R.417 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain A: H.387, P.388, E.389, D.390 Ligands: MG.37 Ligand excluded by PLIP SO4.44: 4 residues within 4Å: Chain B: R.475, Y.479, E.491, A.497 Ligand excluded by PLIP SO4.45: 4 residues within 4Å: Chain B: T.504, A.505, G.506, A.507 Ligand excluded by PLIP SO4.46: 2 residues within 4Å: Chain B: R.90, E.91 Ligand excluded by PLIP SO4.47: 1 residues within 4Å: Chain B: R.478 Ligand excluded by PLIP SO4.48: 3 residues within 4Å: Chain B: R.16, S.57, G.58 Ligand excluded by PLIP SO4.49: 3 residues within 4Å: Chain B: Q.413, R.417, N.533 Ligand excluded by PLIP SO4.50: 3 residues within 4Å: Chain B: T.466, A.467, E.468 Ligand excluded by PLIP SO4.51: 1 residues within 4Å: Chain B: R.136 Ligand excluded by PLIP SO4.52: 4 residues within 4Å: Chain A: R.534 Chain B: R.356, L.360, W.385 Ligand excluded by PLIP SO4.53: 4 residues within 4Å: Chain B: P.108, T.109, S.110, R.143 Ligand excluded by PLIP

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

CL.18: 1 residues within 4Å: Chain A: A.467 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain A: R.177, Q.181 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain A: R.16, G.58 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain A: S.371, D.372 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain A: N.233, P.312, E.313 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain A: N.283, H.287 Ligands: ZN.36 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain A: T.195 Ligand excluded by PLIP CL.25: 1 residues within 4Å: Chain A: R.136 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain A: W.286 Ligands: ZN.36 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain A: R.525, A.526, Q.527 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain A: R.13, E.185, N.186 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Chain A: R.424 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain A: G.240, R.296 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain A: H.387, R.393 Ligands: MG.37 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain A: R.246 Ligands: SO4.11 Ligand excluded by PLIP CL.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain A: N.283, H.284 Ligand excluded by PLIP CL.54: 6 residues within 4Å: Chain A: L.386 Chain B: G.523, R.525, A.526, Q.527 Ligands: MG.73 Ligand excluded by PLIP CL.55: 1 residues within 4Å: Chain B: R.393 Ligand excluded by PLIP CL.56: 1 residues within 4Å: Chain B: R.525 Ligand excluded by PLIP CL.57: 3 residues within 4Å: Chain B: H.387, E.389, D.390 Ligand excluded by PLIP CL.58: 2 residues within 4Å: Chain B: R.219, L.324 Ligand excluded by PLIP CL.59: 1 residues within 4Å: Chain B: L.441 Ligand excluded by PLIP CL.60: 1 residues within 4Å: Chain B: P.36 Ligand excluded by PLIP CL.61: 1 residues within 4Å: Chain B: P.44 Ligand excluded by PLIP CL.62: 4 residues within 4Å: Chain B: G.264, N.265, D.266, T.267 Ligand excluded by PLIP CL.63: 3 residues within 4Å: Chain A: H.381 Chain B: H.381 Ligands: ZN.35 Ligand excluded by PLIP CL.64: 4 residues within 4Å: Chain B: Y.70, S.93, E.94 Ligands: MG.79 Ligand excluded by PLIP CL.65: 2 residues within 4Å: Chain B: S.371, D.372 Ligand excluded by PLIP CL.66: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.67: 1 residues within 4Å: Chain B: H.322 Ligand excluded by PLIP CL.68: 2 residues within 4Å: Chain B: R.246 Ligands: MG.75 Ligand excluded by PLIP CL.69: 2 residues within 4Å: Chain B: R.521, R.522 Ligand excluded by PLIP CL.70: 2 residues within 4Å: Chain B: P.312, E.313 Ligand excluded by PLIP CL.71: 2 residues within 4Å: Chain B: Q.66 Ligands: MG.74 Ligand excluded by PLIP CL.72: 3 residues within 4Å: Chain B: M.241, G.242 Ligands: MG.75 Ligand excluded by PLIP

12 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.37: 5 residues within 4Å: Chain A: H.387, D.390, R.393 Ligands: SO4.17, CL.31 No protein-ligand interaction detected (PLIP) MG.38: 2 residues within 4Å: Chain A: H.387 Chain B: R.522 No protein-ligand interaction detected (PLIP) MG.39: 1 residues within 4Å: Chain A: H.253 No protein-ligand interaction detected (PLIP) MG.40: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.41: 1 residues within 4Å: Chain A: H.284 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.284, H2O.3, H2O.3 MG.73: 5 residues within 4Å: Chain B: R.525, A.526, Q.527, A.528 Ligands: CL.54 No protein-ligand interaction detected (PLIP) MG.74: 2 residues within 4Å: Chain B: Q.66 Ligands: CL.71 No protein-ligand interaction detected (PLIP) MG.75: 5 residues within 4Å: Chain B: G.240, G.242, E.243 Ligands: CL.68, CL.72 No protein-ligand interaction detected (PLIP) MG.76: 2 residues within 4Å: Chain B: P.162, R.245 No protein-ligand interaction detected (PLIP) MG.77: 1 residues within 4Å: Chain B: H.284 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.284 MG.78: 1 residues within 4Å: Chain B: H.253 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.253, H2O.5, H2O.5 MG.79: 2 residues within 4Å: Chain B: S.93 Ligands: CL.64 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nachon, F. et al., Grid-Type Quaternary Metallosupramolecular Compounds Inhibit Human Cholinesterases through Dynamic Multivalent Interactions. Chembiochem (2022)

Release Date

2023-06-21

Peptides

Acetylcholinesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acetylcholinesterase

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