SMTL ID : 6fqn.1

Carbamylated T. californica acetylcholineterase bound to uncharged hybrid reactivator 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x E2W: 6-[4-[(7-chloranyl-1,2,3,4-tetrahydroacridin-9-yl)amino]butyl]-2-[(oxidanylamino)methyl]pyridin-3-ol(Non-covalent)

E2W.1: 10 residues within 4Å: Chain A: Y.67, Q.71, Y.118, W.276, L.279, S.283, I.284, Y.331, G.332 Ligands: P6G.12 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.67, A:Y.67, A:W.276, A:W.276, A:W.276, A:L.279 Hydrogen bonds: A:W.276 Water bridges: A:R.286 pi-Stacking: A:W.276 E2W.14: 10 residues within 4Å: Chain B: Y.67, Q.71, Y.118, W.276, L.279, S.283, I.284, Y.331, G.332 Ligands: P6G.25 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.67, B:Y.67, B:W.276, B:W.276, B:W.276, B:L.279 Hydrogen bonds: B:W.276 Water bridges: B:R.286 pi-Stacking: B:W.276

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

NAG.2: 1 residues within 4Å: Chain A: N.56 No protein-ligand interaction detected (PLIP) NAG.3: 3 residues within 4Å: Chain A: G.412, N.413, G.414 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.413 NAG.4: 2 residues within 4Å: Chain A: E.452, N.454 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.452 NAG.15: 1 residues within 4Å: Chain B: N.56 No protein-ligand interaction detected (PLIP) NAG.16: 3 residues within 4Å: Chain B: G.412, N.413, G.414 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.413 NAG.17: 2 residues within 4Å: Chain B: E.452, N.454 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.452

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: R.239, V.243, L.253, D.256, L.259 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.239, A:D.256 EDO.13: 6 residues within 4Å: Chain A: S.76, M.80, N.426, L.427, V.428, Y.439 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.76, A:V.428 EDO.18: 5 residues within 4Å: Chain B: R.239, V.243, L.253, D.256, L.259 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.239 EDO.26: 6 residues within 4Å: Chain B: S.76, M.80, N.426, L.427, V.428, Y.439 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.76, B:V.428

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

CL.6: 2 residues within 4Å: Chain A: R.41, K.266 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: D.386, W.432 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: H.403, N.522, Q.523 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: Q.497, V.515 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: R.102, F.183 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: H.422, N.503, T.504, E.505 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: R.41, K.266 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: D.386, W.432 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: H.403, N.522, Q.523 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain B: Q.497, V.515 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: R.102, F.183 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: H.422, N.503, T.504, E.505 Ligand excluded by PLIP

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.12: 12 residues within 4Å: Chain A: W.81, G.114, G.115, Y.118, E.196, S.197, E.324, F.327, F.328, Y.331, H.437 Ligands: E2W.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.115, A:E.324, A:F.327, A:F.328 P6G.25: 12 residues within 4Å: Chain B: W.81, G.114, G.115, Y.118, E.196, S.197, E.324, F.327, F.328, Y.331, H.437 Ligands: E2W.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.69, B:G.115, B:E.324, B:F.327, B:F.328 Water bridges: B:Y.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Santoni, G. et al., Structure-Based Optimization of Nonquaternary Reactivators of Acetylcholinesterase Inhibited by Organophosphorus Nerve Agents. J. Med. Chem. (2018)

Release Date

2018-08-29

Peptides

Acetylcholinesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Acetylcholinesterase

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