SMTL ID : 7qyn.1

Mus musculus acetylcholinesterase in complex with 2-((hydroxyimino)methyl)-1-(5-(4-methyl-3-nitrobenzamido)pentyl)pyridinium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: G.345, S.347, N.350, L.353 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.345, A:S.347 Water bridges: A:L.353 NAG.2: 2 residues within 4Å: Chain A: S.462, N.464 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.462, A:N.464 NAG.11: 4 residues within 4Å: Chain B: G.345, S.347, N.350, L.353 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.345, B:S.347 Water bridges: B:L.353 NAG.12: 2 residues within 4Å: Chain B: S.462, N.464 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.462, B:N.464

2 x I1X: 4-methyl-3-nitro-~{N}-[(2~{E},4~{E})-5-[2-[(oxidanylamino)methyl]pyridin-1-yl]penta-2,4-dienyl]benzamide(Non-covalent)

I1X.3: 15 residues within 4Å: Chain A: Y.72, W.86, G.121, G.122, Y.124, S.203, A.204, E.285, W.286, F.297, S.298, Y.337, F.338, Y.341, H.447 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.72, A:E.285, A:W.286, A:F.297, A:Y.337, A:Y.337, A:F.338, A:Y.341 Hydrogen bonds: A:G.121, A:G.122, A:Y.124, A:S.203, A:A.204, A:H.447 Water bridges: A:R.296 pi-Stacking: A:Y.72, A:W.86, A:W.86, A:Y.124, A:W.286, A:W.286 I1X.13: 15 residues within 4Å: Chain B: Y.72, W.86, G.121, G.122, Y.124, S.203, A.204, E.285, W.286, F.297, S.298, Y.337, F.338, Y.341, H.447 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.72, B:Y.72, B:W.86, B:E.285, B:W.286, B:F.297, B:Y.337, B:Y.337, B:F.338 Hydrogen bonds: B:G.121, B:G.122, B:S.203, B:A.204, B:H.447 Water bridges: B:R.296 pi-Stacking: B:Y.124, B:W.286, B:W.286

11 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.4: 4 residues within 4Å: Chain A: D.304, G.305, S.309, D.310 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.310 PG0.5: 2 residues within 4Å: Chain A: Q.140, V.141 No protein-ligand interaction detected (PLIP) PG0.6: 5 residues within 4Å: Chain A: G.43, R.274, T.275, R.276, P.277 No protein-ligand interaction detected (PLIP) PG0.7: 4 residues within 4Å: Chain A: I.20, T.63, T.64, F.65 No protein-ligand interaction detected (PLIP) PG0.8: 4 residues within 4Å: Chain A: H.381, T.383, D.384 Chain B: Q.527 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.385 PG0.9: 3 residues within 4Å: Chain A: D.333, D.396, W.442 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.395 PG0.10: 3 residues within 4Å: Chain A: S.57, V.59, L.60 No protein-ligand interaction detected (PLIP) PG0.14: 4 residues within 4Å: Chain B: A.412, Q.413, N.533, R.534 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.413, B:N.533 PG0.15: 5 residues within 4Å: Chain B: K.332, D.333, D.396, L.441, W.442 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.332 PG0.16: 4 residues within 4Å: Chain B: V.303, D.304, G.305, S.309 No protein-ligand interaction detected (PLIP) PG0.17: 4 residues within 4Å: Chain B: P.88, N.89, R.90, E.91 No protein-ligand interaction detected (PLIP)

2 x TOE: 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL(Non-covalent)

TOE.18: 7 residues within 4Å: Chain B: R.11, V.12, R.13, E.185, N.186, A.188, A.189 No protein-ligand interaction detected (PLIP) TOE.19: 4 residues within 4Å: Chain A: Q.527 Chain B: H.381, Y.382, D.384 No protein-ligand interaction detected (PLIP)

1 x P15: 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL(Non-covalent)

P15.20: 12 residues within 4Å: Chain A: A.377, L.380, H.381, Q.527, F.531, F.535 Chain B: A.377, L.380, H.381, Q.527, F.531, F.535 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:T.528 Hydrogen bonds: A:Q.527

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

CL.21: 1 residues within 4Å: Chain B: K.53 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lindgren, C. et al., Broad-Spectrum Antidote Discovery by Untangling the Reactivation Mechanism of Nerve-Agent-Inhibited Acetylcholinesterase. Chemistry (2022)

Release Date

2022-04-27

Peptides

Acetylcholinesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acetylcholinesterase

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