SMTL ID : 7r2f.1

Structure of tabun inhibited acetylcholinesterase in complex with 2-((hydroxyimino)methyl)-1-(5-(4-methyl-3-nitrobenzamido)pentyl)pyridinium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 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

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: 10 residues within 4Å: Chain A: Y.72, Y.124, E.285, W.286, L.289, R.296, F.297, S.298, F.338, Y.341 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:E.285, A:W.286, A:F.297, A:F.338 Hydrogen bonds: A:W.286 pi-Stacking: A:Y.72, A:Y.124, A:W.286, A:W.286 I1X.10: 9 residues within 4Å: Chain B: Y.72, Y.124, E.285, W.286, F.297, S.298, Y.337, F.338, Y.341 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.72, B:Y.72, B:E.285, B:W.286, B:F.297, B:F.338, B:Y.341 Hydrogen bonds: B:Y.124 pi-Stacking: B:Y.124, B:W.286, B:W.286

14 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.413, N.533 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.533 PG0.6: 6 residues within 4Å: Chain A: H.381, Y.382, T.383, D.384, H.393 Chain B: Q.527 No protein-ligand interaction detected (PLIP) PG0.7: 6 residues within 4Å: Chain A: E.431, H.432, R.433, N.514, L.515, K.516 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.433, A:L.515 PG0.8: 4 residues within 4Å: Chain A: D.333, D.396, L.441, W.442 No protein-ligand interaction detected (PLIP) PG0.9: 2 residues within 4Å: Chain A: R.3, D.5 No protein-ligand interaction detected (PLIP) PG0.11: 4 residues within 4Å: Chain A: Q.527 Chain B: H.381, Y.382, D.384 No protein-ligand interaction detected (PLIP) PG0.12: 4 residues within 4Å: Chain B: Q.413, R.417, N.533, R.534 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.413, B:R.417, B:N.533 PG0.13: 4 residues within 4Å: Chain B: K.332, D.333, D.396, W.442 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.332 PG0.14: 6 residues within 4Å: Chain B: T.112, P.113, E.142, G.143, A.144, R.485 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.485 PG0.15: 3 residues within 4Å: Chain B: D.304, G.305, D.310 No protein-ligand interaction detected (PLIP) PG0.16: 3 residues within 4Å: Chain B: E.185, A.188, A.189 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.189 PG0.17: 3 residues within 4Å: Chain B: R.224, Q.325, T.486 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.325 PG0.18: 2 residues within 4Å: Chain B: N.89, R.90 No protein-ligand interaction detected (PLIP)

1 x 7PG: 2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL(Non-covalent)

7PG.19: 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 A, 1 interactions with chain B Hydrogen bonds: A:Q.527, B:Q.527

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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