SMTL ID : 7r4e.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

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.1: 10 residues within 4Å: Chain A: Y.72, Y.124, E.285, W.286, R.296, F.297, S.298, Y.337, F.338, Y.341 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.72, A:E.285, A:W.286, A:Y.337, A:F.338 Hydrogen bonds: A:Y.124, A:W.286 pi-Stacking: A:Y.124, A:W.286, A:W.286 I1X.9: 8 residues within 4Å: Chain B: Y.72, Y.124, E.285, W.286, F.297, S.298, F.338, Y.341 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.72, B:Y.72, B:W.286, B:F.297 Hydrogen bonds: B:Y.124, B:W.286 pi-Stacking: B:Y.124, B:W.286, B:W.286

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

NAG.2: 4 residues within 4Å: Chain A: G.345, S.347, N.350, L.353 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.345 Water bridges: A:E.351 NAG.3: 1 residues within 4Å: Chain A: N.464 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.464 NAG.10: 4 residues within 4Å: Chain B: G.345, S.347, N.350, L.353 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.345, B:S.347 NAG.11: 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

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

PG0.4: 5 residues within 4Å: Chain A: V.303, D.304, G.305, S.309, D.310 No protein-ligand interaction detected (PLIP) PG0.5: 7 residues within 4Å: Chain A: H.381, Y.382, T.383, D.384, H.393 Chain B: Q.527 Ligands: P15.8 No protein-ligand interaction detected (PLIP) PG0.12: 3 residues within 4Å: Chain B: Q.413, N.533, R.534 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.413, B:N.533 PG0.13: 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 PG0.14: 4 residues within 4Å: Chain B: D.304, G.305, S.309, D.310 No protein-ligand interaction detected (PLIP)

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

TOE.6: 6 residues within 4Å: Chain A: K.332, D.333, E.351, R.395, L.441, W.442 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.351, A:R.395 Water bridges: A:W.442 TOE.7: 7 residues within 4Å: Chain A: Q.527 Chain B: H.381, Y.382, D.384, A.397, A.400 Ligands: P15.8 No protein-ligand interaction detected (PLIP) TOE.15: 5 residues within 4Å: Chain B: R.11, R.13, E.185, A.188, A.189 No protein-ligand interaction detected (PLIP)

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

P15.8: 14 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 Ligands: PG0.5, TOE.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.381, B:Q.527 Water bridges: B:T.528

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

Related Entries With Identical Sequence