SMTL ID : 8aev.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.89 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: 4 residues within 4Å: Chain B: P.344, G.345, S.347, N.350 1 PLIP interactions: 1 interactions with chain B 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: 3 residues within 4Å: Chain A: N.265, T.267, E.268 No protein-ligand interaction detected (PLIP)

1 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-covalent)

GAL-SIA.3: 8 residues within 4Å: Chain B: P.49, P.50, L.174, R.177, L.178, Q.181, P.217, D.306 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.217, B:P.50, B:L.178, B:Q.181, B:D.306 Hydrophobic interactions: B:P.49 Salt bridges: B:R.177

1 x LWU: 1-(2-(2-((6-(dihydroxymethyl)-2-phenylpyrimidin-4-yl)methylene)hydrazineyl)-2-oxoethyl)pyridin-1-ium(Non-covalent)

LWU.5: 15 residues within 4Å: Chain A: Y.72, W.86, Y.124, E.202, X.203, W.286, S.293, V.294, F.295, R.296, F.297, Y.337, F.338, Y.341, H.447 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.72 Hydrogen bonds: A:Y.124, A:Y.124, A:S.293, A:R.296, A:Y.337, A:Y.337 Water bridges: A:S.125 pi-Stacking: A:W.86, A:W.86, A:W.286, A:W.286, A:Y.341

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

SO4.6: 4 residues within 4Å: Chain A: Q.413, R.417, N.533 Ligands: MG.34 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: L.386, H.387, P.388, E.389, D.390 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: T.504, G.506, A.507 Ligand excluded by PLIP SO4.9: 1 residues within 4Å: Chain A: H.322 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain A: G.240, M.241, G.242, E.243 Ligands: MG.37 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain A: F.80, K.348 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: N.317, R.417 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: V.520, R.521, R.522 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain A: R.493, D.494, P.495 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain B: Q.413, R.417, N.533, R.534 Ligand excluded by PLIP SO4.40: 4 residues within 4Å: Chain B: T.504, A.505, G.506, A.507 Ligand excluded by PLIP SO4.41: 5 residues within 4Å: Chain A: R.534 Chain B: R.356, L.360, W.385 Ligands: MG.33 Ligand excluded by PLIP SO4.42: 1 residues within 4Å: Chain B: R.478 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain B: R.16, S.57, G.58 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain B: K.23, R.136 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain A: R.522 Chain B: H.387, R.393 Ligand excluded by PLIP

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

CL.15: 1 residues within 4Å: Chain A: A.467 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain A: R.177 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain A: R.16, G.58 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain A: D.372 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain A: N.233, P.312, E.313 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain A: K.23, R.136 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain A: R.525, A.526, Q.527 Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain A: R.424 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain A: G.240, E.243 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain A: R.356 Ligands: MG.32 Ligand excluded by PLIP CL.25: 1 residues within 4Å: Chain A: H.284 Ligand excluded by PLIP CL.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.27: 1 residues within 4Å: Chain A: Y.72 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain A: T.109, S.110, R.143 Ligand excluded by PLIP CL.46: 6 residues within 4Å: Chain A: L.386 Chain B: G.523, R.525, A.526, Q.527 Ligands: MG.66 Ligand excluded by PLIP CL.47: 1 residues within 4Å: Chain B: R.393 Ligand excluded by PLIP CL.48: 1 residues within 4Å: Chain B: R.525 Ligand excluded by PLIP CL.49: 2 residues within 4Å: Chain B: H.387, E.389 Ligand excluded by PLIP CL.50: 1 residues within 4Å: Chain B: R.219 Ligand excluded by PLIP CL.51: 2 residues within 4Å: Chain B: P.36, Y.98 Ligand excluded by PLIP CL.52: 1 residues within 4Å: Chain B: P.44 Ligand excluded by PLIP CL.53: 2 residues within 4Å: Chain B: G.264, T.267 Ligand excluded by PLIP CL.54: 1 residues within 4Å: Ligands: MG.67 Ligand excluded by PLIP CL.55: 2 residues within 4Å: Chain B: R.521, R.522 Ligand excluded by PLIP CL.56: 2 residues within 4Å: Chain B: N.233, E.313 Ligand excluded by PLIP CL.57: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.58: 1 residues within 4Å: Chain B: R.424 Ligand excluded by PLIP CL.59: 2 residues within 4Å: Chain B: P.277, A.278 Ligand excluded by PLIP CL.60: 4 residues within 4Å: Chain B: P.108, T.109, S.110, R.143 Ligand excluded by PLIP CL.61: 3 residues within 4Å: Chain B: M.241, G.242 Ligands: MG.67 Ligand excluded by PLIP CL.62: 1 residues within 4Å: Chain B: R.475 Ligand excluded by PLIP

5 x ZN: ZINC ION(Non-covalent)

ZN.29: 2 residues within 4Å: Chain A: H.381 Chain B: H.381 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.381, B:H.381 ZN.30: 1 residues within 4Å: Chain A: H.284 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.284 ZN.63: 2 residues within 4Å: Chain A: H.381 Chain B: H.381 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.381 ZN.64: 1 residues within 4Å: Chain B: H.322 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.322 ZN.65: 1 residues within 4Å: Chain B: X.203 No protein-ligand interaction detected (PLIP)

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

MG.31: 1 residues within 4Å: Chain A: H.253 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.253 MG.32: 1 residues within 4Å: Ligands: CL.24 No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Chain A: R.534 Ligands: SO4.41 No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Chain A: N.533 Ligands: SO4.6 No protein-ligand interaction detected (PLIP) MG.35: 1 residues within 4Å: Chain A: E.185 No protein-ligand interaction detected (PLIP) MG.36: 2 residues within 4Å: Chain A: T.436, E.452 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.452, H2O.3 MG.37: 1 residues within 4Å: Ligands: SO4.10 No protein-ligand interaction detected (PLIP) MG.38: 3 residues within 4Å: Chain A: D.488, N.490, Q.499 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.488 MG.66: 5 residues within 4Å: Chain B: R.525, A.526, Q.527, A.528 Ligands: CL.46 No protein-ligand interaction detected (PLIP) MG.67: 5 residues within 4Å: Chain B: G.240, G.242, E.243 Ligands: CL.54, CL.61 No protein-ligand interaction detected (PLIP) MG.68: 2 residues within 4Å: Chain B: M.241, R.245 No protein-ligand interaction detected (PLIP) MG.69: 1 residues within 4Å: Chain B: H.253 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.253 MG.70: 3 residues within 4Å: Chain B: M.85, T.436, E.452 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.452, H2O.6 MG.71: 2 residues within 4Å: Chain B: S.371, D.372 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

2023-06-14

Peptides

Acetylcholinesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acetylcholinesterase