SMTL ID : 7p1p.1

Crystal structure of human acetylcholinesterase in complex with (E)-3-hydroxy-6-(3-(4-(4-(((2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)oxy)butyl)-1H-1,2,3-triazol-1-yl)propyl)picolinaldehyde oxime

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.03 Å

Oligo State

hetero-2-2-mer

Ligands

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.1: 6 residues within 4Å: Chain B: A.82, P.83, G.84, S.86, N.89, L.92 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.86, B:G.84

1 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.2: 4 residues within 4Å: Chain D: G.84, S.86, N.89, L.92 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.86

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 C: P.48, P.49, P.51, L.173, R.176, Q.180, E.184, P.216 Chain D: D.45 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:P.216, D:D.45, D:D.45, C:Q.180 Salt bridges: C:R.176

1 x 4IX: (2R,3R,4S,5S,6R)-2-[4-[1-[3-[6-[(Z)-hydroxyiminomethyl]-5-oxidanyl-pyridin-2-yl]propyl]-1,2,3-triazol-4-yl]butoxy]-6-(hydroxymethyl)oxane-3,4,5-triol(Non-covalent)

4IX.4: 16 residues within 4Å: Chain A: W.85, G.119, G.120, G.121, Y.123, E.201, S.202 Chain B: W.25, L.28, Q.30, E.31, F.36, Y.76, F.77, Y.80, H.186 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.25, B:W.25, B:F.36, B:F.36, B:Y.76 Hydrogen bonds: B:L.28, B:Q.30, A:G.119, A:G.120, A:G.121, A:S.202 pi-Stacking: B:F.77

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

SO4.5: 3 residues within 4Å: Chain A: G.239, M.240, G.241 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.240, A:G.241 SO4.6: 1 residues within 4Å: Chain A: R.89 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.89 SO4.7: 3 residues within 4Å: Chain A: L.21, K.22, R.135 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.22, A:R.135 SO4.11: 3 residues within 4Å: Chain B: T.243, G.245, A.246 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.243, B:G.245, B:A.246 SO4.12: 2 residues within 4Å: Chain B: N.56, R.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.56 Salt bridges: B:R.156 SO4.13: 5 residues within 4Å: Chain B: R.95, L.99, V.118, W.124 Chain D: R.273 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Salt bridges: B:R.95, D:R.273 SO4.14: 1 residues within 4Å: Chain B: H.61 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.61 SO4.15: 4 residues within 4Å: Chain B: Q.152, R.156, N.272, R.273 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.152 Water bridges: B:N.56, B:Q.152 Salt bridges: B:R.156 SO4.16: 2 residues within 4Å: Chain B: S.110, D.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.111 SO4.24: 3 residues within 4Å: Chain C: R.15, S.56, G.57 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.57 Salt bridges: C:R.15 SO4.25: 1 residues within 4Å: Chain C: R.135 2 PLIP interactions: 2 interactions with chain C Water bridges: C:K.22 Salt bridges: C:R.135 SO4.30: 4 residues within 4Å: Chain D: T.243, A.244, G.245, A.246 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.243, D:G.245, D:A.246 SO4.31: 6 residues within 4Å: Chain B: R.273 Chain D: R.95, L.99, V.118, W.124 Ligands: MG.34 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Salt bridges: B:R.273, D:R.95 SO4.32: 4 residues within 4Å: Chain D: Q.152, R.156, N.272, R.273 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.272 Salt bridges: D:R.156 SO4.33: 3 residues within 4Å: Chain C: R.45 Chain D: P.16, A.17 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:A.17, C:R.45

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

CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: R.15, G.57 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: F.79 Chain B: K.87 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: R.264, A.267 Ligand excluded by PLIP CL.19: 1 residues within 4Å: Chain B: R.163 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain A: N.232 Chain B: T.50, P.51, E.52 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain B: R.261 Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain B: R.132 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: H.126, D.129 Ligand excluded by PLIP CL.27: 1 residues within 4Å: Ligands: MG.26 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain C: M.240, G.241 Ligands: MG.26 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain C: P.107, T.108 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain C: Y.123 Chain D: Y.76, Y.80 Ligand excluded by PLIP CL.37: 1 residues within 4Å: Chain D: R.261 Ligand excluded by PLIP CL.38: 4 residues within 4Å: Chain D: R.264, A.265, Q.266, A.267 Ligand excluded by PLIP CL.39: 1 residues within 4Å: Chain D: D.111 Ligand excluded by PLIP CL.40: 1 residues within 4Å: Chain D: R.132 Ligand excluded by PLIP CL.41: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.42: 3 residues within 4Å: Chain D: H.120, Q.266, F.270 Ligand excluded by PLIP CL.43: 3 residues within 4Å: Chain D: H.126, E.128, D.129 Ligand excluded by PLIP CL.44: 2 residues within 4Å: Chain C: F.79 Chain D: K.87 Ligand excluded by PLIP CL.45: 1 residues within 4Å: Chain D: R.217 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.17: 6 residues within 4Å: Chain B: A.116, L.119, H.120, F.270 Chain D: L.119, H.120 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Metal complexes: D:H.120, B:H.120 MG.26: 5 residues within 4Å: Chain C: G.239, G.241, E.242 Ligands: CL.27, CL.28 No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Chain D: R.95 Ligands: SO4.31 No protein-ligand interaction detected (PLIP) MG.35: 2 residues within 4Å: Chain C: N.232 Chain D: E.52 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Da Silva, O. et al., A New Class of Bi- and Trifunctional Sugar Oximes as Antidotes against Organophosphorus Poisoning. J.Med.Chem. (2022)

Release Date

2021-12-29

Peptides

Acetylcholinesterase: AC
Acetylcholinesterase: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
aa

C
bb

B
A

D
B

Acetylcholinesterase

Acetylcholinesterase

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