SMTL ID : 7p1n.1

Crystal structure of human acetylcholinesterase in complex with (2R,3R,4S,5S,6R)-2-{4-[1-(4-{5-hydroxy-6-[(E)-(hydroxyimino)methyl]pyridin-2-yl}butyl)-1H-1,2,3-triazol-4-yl]butoxy}-6-(hydroxymethyl)oxane-3,4,5-triol oxime

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 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: 5 residues within 4Å: Chain D: G.84, F.85, S.86, N.89, L.92 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: 10 residues within 4Å: Chain C: P.48, P.49, P.51, P.167, L.173, R.176, Q.180, E.184, P.216 Chain D: D.45 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.180, C:P.216, C:Q.180 Salt bridges: C:R.176

2 x 4J1: (2R,3R,4S,5S,6R)-2-[4-[1-[4-[6-[(Z)-hydroxyiminomethyl]-5-oxidanyl-pyridin-2-yl]butyl]-1,2,3-triazol-4-yl]butoxy]-6-(hydroxymethyl)oxane-3,4,5-triol(Non-covalent)

4J1.4: 15 residues within 4Å: Chain A: Y.71, W.85, G.120, G.121, Y.123, E.201, S.202, A.203 Chain B: W.25, H.26, F.36, Y.76, F.77, Y.80, H.186 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.25, B:F.36, B:Y.76, B:F.77, B:Y.80 Hydrogen bonds: B:H.26, A:G.120, A:G.121, A:S.202, A:A.203 Water bridges: B:R.35, A:G.119 pi-Stacking: B:Y.80 4J1.5: 10 residues within 4Å: Chain A: P.110, Q.183, D.192, P.193, T.194, S.195, V.196, G.219, F.221, H.222 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.193, A:T.194 Hydrogen bonds: A:Q.183, A:V.196, A:F.221, A:H.222

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

SO4.6: 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 SO4.7: 1 residues within 4Å: Chain A: R.135 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.135 SO4.14: 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 SO4.15: 2 residues within 4Å: Chain B: N.56, R.156 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.156 SO4.16: 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 D, 1 interactions with chain B Salt bridges: D:R.273, B:R.95 SO4.17: 1 residues within 4Å: Chain B: H.61 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.61 SO4.18: 3 residues within 4Å: Chain B: Q.152, R.156, N.272 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.152 Water bridges: B:Q.152, B:R.156 Salt bridges: B:R.156 SO4.19: 2 residues within 4Å: Chain B: S.110, D.111 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.111, B:D.111 SO4.29: 1 residues within 4Å: Chain C: R.135 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.135 SO4.30: 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 SO4.37: 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 SO4.38: 5 residues within 4Å: Chain B: R.273 Chain D: R.95, L.99, W.124 Ligands: MG.40 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Salt bridges: D:R.95, B:R.273 SO4.39: 4 residues within 4Å: Chain D: Q.152, R.156, N.272, R.273 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.156

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

CL.8: 1 residues within 4Å: Chain A: R.176 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.11: 2 residues within 4Å: Chain A: T.108, R.142 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: H.222, R.223 Chain B: Q.64 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: R.264, Q.266, A.267 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain B: R.163 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain B: P.51, E.52 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain B: R.260, R.261 Ligand excluded by PLIP CL.26: 1 residues within 4Å: Chain B: R.132 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain B: H.126, E.128, D.129 Ligands: MG.21 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain B: R.202 Ligand excluded by PLIP CL.32: 1 residues within 4Å: Ligands: MG.31 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain C: Y.123 Chain D: Y.76, F.77, Y.80 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain C: M.240, G.241 Ligands: MG.31 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain C: P.107, T.108, S.109 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain C: F.79 Chain D: K.87 Ligand excluded by PLIP CL.42: 2 residues within 4Å: Chain D: R.260, R.261 Ligand excluded by PLIP CL.43: 2 residues within 4Å: Chain D: Q.266, A.267 Ligand excluded by PLIP CL.44: 1 residues within 4Å: Chain D: D.111 Ligand excluded by PLIP CL.45: 2 residues within 4Å: Chain D: H.126, R.132 Ligand excluded by PLIP CL.46: 1 residues within 4Å: Chain D: R.264 Ligand excluded by PLIP CL.47: 3 residues within 4Å: Chain D: H.120, Q.266, F.270 Ligand excluded by PLIP CL.48: 3 residues within 4Å: Chain D: H.126, E.128, D.129 Ligand excluded by PLIP CL.49: 1 residues within 4Å: Chain D: R.217 Ligand excluded by PLIP CL.50: 2 residues within 4Å: Chain D: P.16, A.17 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 2 residues within 4Å: Chain A: T.63, R.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.89, A:R.89

5 x MG: MAGNESIUM ION(Non-covalent)

MG.20: 4 residues within 4Å: Chain B: A.116, H.120, F.270 Chain D: H.120 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Metal complexes: D:H.120, B:H.120 MG.21: 3 residues within 4Å: Chain B: H.126, D.129 Ligands: CL.27 No protein-ligand interaction detected (PLIP) MG.31: 5 residues within 4Å: Chain C: G.239, G.241, E.242 Ligands: CL.32, CL.34 No protein-ligand interaction detected (PLIP) MG.40: 2 residues within 4Å: Chain D: R.95 Ligands: SO4.38 No protein-ligand interaction detected (PLIP) MG.41: 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

2022-06-08

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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