SMTL ID : 6f25.1

Crystal structure of human acetylcholinesterase in complex with C35.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.05 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.339, P.340, G.341, F.342, S.343, N.346, L.349 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.341 NAG-NAG-FUC.3: 4 residues within 4Å: Chain B: P.340, G.341, S.343, N.346 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.343, B:S.343

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 4 residues within 4Å: Chain A: N.261, T.263, E.264 Ligands: CL.24 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: S.458, N.460 No protein-ligand interaction detected (PLIP)

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

SO4.5: 2 residues within 4Å: Chain A: T.462, A.463 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.463, A:E.464 SO4.6: 2 residues within 4Å: Chain A: Q.409, R.413 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.409 Water bridges: A:N.529 Salt bridges: A:R.413, A:R.530 SO4.7: 3 residues within 4Å: Chain A: R.352, L.356 Chain B: R.530 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.530, A:R.352 SO4.8: 3 residues within 4Å: Chain A: T.500, G.502, A.503 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.500, A:G.502, A:A.503 SO4.9: 1 residues within 4Å: Chain A: H.318 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.318 SO4.10: 3 residues within 4Å: Chain A: G.236, M.237, G.238 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.237, A:G.238 SO4.28: 4 residues within 4Å: Chain B: T.500, A.501, G.502, A.503 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.500, B:A.501, B:G.502, B:A.503 SO4.29: 4 residues within 4Å: Chain A: R.530 Chain B: R.352, L.356, W.381 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.530, B:R.352 SO4.30: 1 residues within 4Å: Chain B: R.474 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.474 SO4.31: 3 residues within 4Å: Chain B: G.236, M.237, G.238 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.237, B:G.238 Water bridges: B:E.239, B:E.239 SO4.32: 3 residues within 4Å: Chain B: Q.409, R.413, R.530 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.409 Water bridges: B:N.529 Salt bridges: B:R.413 SO4.33: 5 residues within 4Å: Chain B: P.102, P.104, T.105, S.106, T.108 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.105, B:T.105, B:S.106 Salt bridges: B:R.139

2 x CVZ: 3-[(~{E})-5-[ethyl-[(2-nitrophenyl)methyl]amino]pent-1-enyl]-1-[5-[ethyl-[(2-nitrophenyl)methyl]amino]pentyl]-6-methyl-pyrimidine-2,4-dione(Non-covalent)

CVZ.11: 18 residues within 4Å: Chain A: Y.68, G.78, W.82, G.117, Y.120, E.198, S.199, W.282, H.283, S.289, V.290, F.291, F.293, Y.333, F.334, Y.337, W.435, H.443 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.82, A:V.290, A:F.334, A:Y.337, A:Y.337, A:W.435 Hydrogen bonds: A:Y.120, A:Y.333 pi-Stacking: A:W.82, A:W.282, A:H.283 CVZ.34: 16 residues within 4Å: Chain B: G.78, W.82, G.117, Y.120, E.198, S.199, W.282, H.283, P.286, Q.287, E.288, S.289, Y.333, F.334, Y.337, H.443 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.82, B:W.282, B:W.282, B:H.283, B:E.288, B:F.334, B:F.334, B:Y.337, B:Y.337, B:Y.337 Hydrogen bonds: B:Y.120, B:Y.333 Water bridges: B:D.70, B:Y.120 pi-Stacking: B:W.82, B:W.282

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

CL.12: 1 residues within 4Å: Chain A: Q.177 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain A: R.420 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: L.437 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: R.12, G.54 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: T.105, S.106, R.139 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain A: D.368 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain A: R.132 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain A: H.383, E.385, D.386 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain A: H.383, R.389 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain A: R.530, K.534 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain A: F.76, K.344 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain A: N.229, P.308, E.309 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain A: R.161, T.263 Ligands: NAG-NAG.2 Ligand excluded by PLIP CL.25: 1 residues within 4Å: Chain A: R.413 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain A: R.517, R.518 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain A: R.521, Q.523, A.524 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain B: P.158, R.241 Ligand excluded by PLIP CL.36: 1 residues within 4Å: Chain B: R.389 Ligand excluded by PLIP CL.37: 1 residues within 4Å: Chain B: R.521 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain B: K.19, R.132 Ligand excluded by PLIP CL.39: 1 residues within 4Å: Chain B: K.49 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain B: H.383, E.385, D.386 Ligand excluded by PLIP CL.41: 1 residues within 4Å: Chain B: R.389 Ligand excluded by PLIP CL.42: 2 residues within 4Å: Chain B: R.12, G.54 Ligand excluded by PLIP CL.43: 2 residues within 4Å: Chain B: R.215, L.320 Ligand excluded by PLIP CL.44: 3 residues within 4Å: Chain B: R.521, Q.523, A.524 Ligand excluded by PLIP CL.45: 2 residues within 4Å: Chain B: P.436, L.437 Ligand excluded by PLIP CL.46: 2 residues within 4Å: Chain B: A.493, Q.495 Ligand excluded by PLIP CL.47: 3 residues within 4Å: Chain B: G.238, E.239, R.242 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zueva, I. et al., New evidence for dual binding site inhibitors of acetylcholinesterase as improved drugs for treatment of Alzheimer's disease. Neuropharmacology (2019)

Release Date

2018-12-12

Peptides

Acetylcholinesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acetylcholinesterase

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