SMTL ID : 6fld.1

Carbamylated T. californica acetylcholineterase bound to uncharged hybrid reactivator 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: N.56, S.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.58 NAG.2: 4 residues within 4Å: Chain A: G.412, N.413, L.491 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.491 Hydrogen bonds: A:N.413 NAG.3: 2 residues within 4Å: Chain A: E.452, N.454 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.452, A:N.454 NAG.14: 2 residues within 4Å: Chain B: N.56, S.58 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.58 NAG.15: 4 residues within 4Å: Chain B: G.412, N.413, L.491 Ligands: EDO.24 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.491 Hydrogen bonds: B:N.413 NAG.16: 2 residues within 4Å: Chain B: E.452, N.454 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.452, B:N.454

2 x DQ5: 2-[(~{E})-hydroxyiminomethyl]-6-[4-(1,2,3,4-tetrahydroacridin-9-ylamino)butyl]pyridin-3-ol(Non-covalent)

DQ5.4: 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: 1PG.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.67, A:W.276, A:W.276, A:L.279 Hydrogen bonds: A:Y.67 Water bridges: A:Q.71 pi-Stacking: A:W.276, A:W.276 DQ5.17: 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: 1PG.18 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.67, B:W.276, B:W.276, B:L.279 Hydrogen bonds: B:Y.67 Water bridges: B:Q.71 pi-Stacking: B:W.276, B:W.276

2 x 1PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL(Non-covalent)

1PG.5: 10 residues within 4Å: Chain A: W.81, G.114, G.115, E.196, S.197, F.327, F.328, Y.331, H.437 Ligands: DQ5.4 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.324, A:F.328, A:H.437, A:H.437 1PG.18: 10 residues within 4Å: Chain B: W.81, G.114, G.115, E.196, S.197, F.327, F.328, Y.331, H.437 Ligands: DQ5.17 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.118, B:E.324, B:F.328

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

CL.6: 4 residues within 4Å: Chain A: H.403, N.406, N.522, Q.523 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: V.357, P.358, H.359, A.360 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: R.213, N.310, K.313 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: V.19, L.20, Y.131 Ligand excluded by PLIP CL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain B: H.403, N.406, N.522, Q.523 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: V.357, P.358, H.359, A.360 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: R.213, N.310, K.313 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: V.19, L.20, Y.131 Ligand excluded by PLIP CL.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

EDO.11: 5 residues within 4Å: Chain A: T.409, L.491, T.493, T.494 Ligands: NAG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.494, A:T.494 Water bridges: A:G.414 EDO.12: 4 residues within 4Å: Chain A: P.334, G.335, F.336, S.337 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.335, A:F.336 Water bridges: A:L.330, A:G.335, A:F.336, A:F.336 EDO.13: 2 residues within 4Å: Chain A: S.52, V.54 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.52, A:N.56 EDO.24: 5 residues within 4Å: Chain B: T.409, L.491, T.493, T.494 Ligands: NAG.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.494, B:T.494, B:T.494 Water bridges: B:G.414 EDO.25: 4 residues within 4Å: Chain B: P.334, G.335, F.336, S.337 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.335, B:F.336 Water bridges: B:L.330, B:G.335, B:F.336, B:F.336 EDO.26: 2 residues within 4Å: Chain B: S.52, V.54 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.52, B:N.56

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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