SMTL ID : 6g4o.1

Non-aged form of Torpedo californica acetylcholinesterase inhibited by tabun analog NEDPA bound to uncharged reactivator 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.59, S.61, T.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.59, A:S.61 NAG.2: 1 residues within 4Å: Chain A: N.416 No protein-ligand interaction detected (PLIP) NAG.11: 2 residues within 4Å: Chain B: N.59, S.61 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.61 NAG.12: 3 residues within 4Å: Chain B: G.415, N.416, G.417 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.416 NAG.14: 2 residues within 4Å: Chain B: E.455, N.457 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.455, B:E.455, B:N.457

2 x ELT: ethoxy-~{N},~{N}-dimethyl-phosphonamidic acid(Covalent)

ELT.3: 10 residues within 4Å: Chain A: G.117, G.118, G.119, S.200, A.201, W.233, F.290, F.331, H.440 Ligands: PG4.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.331 Hydrogen bonds: A:G.118, A:G.119, A:A.201 pi-Cation interactions: A:W.233 ELT.13: 11 residues within 4Å: Chain B: G.117, G.118, G.119, Y.121, S.200, A.201, W.233, F.288, F.290, H.440 Ligands: P6G.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.118, B:G.119, B:A.201

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

DQ5.4: 7 residues within 4Å: Chain A: Y.70, Y.121, W.279, I.287, Y.334, G.335 Ligands: PG4.7 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.70, A:Y.70, A:W.279, A:W.279, A:W.279, A:W.279 Hydrogen bonds: A:W.279 pi-Stacking: A:W.279

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

CL.5: 1 residues within 4Å: Chain A: Q.500 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: Y.134 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: R.216 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: N.506 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: H.264 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: K.133, Y.134 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain B: L.256 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: T.496, T.497 Ligand excluded by PLIP

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.7: 11 residues within 4Å: Chain A: W.84, G.117, G.118, Y.121, E.199, S.200, F.330, Y.334, H.440 Ligands: ELT.3, DQ5.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.118, A:S.200

1 x NA: SODIUM ION(Non-functional Binders)

NA.16: 2 residues within 4Å: Chain B: S.258, D.259 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.259

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

P6G.19: 11 residues within 4Å: Chain B: W.84, G.118, Y.121, E.199, W.279, F.290, F.330, F.331, Y.334, H.440 Ligands: ELT.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.121 Water bridges: B:E.199, B:E.199

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
B

Acetylcholinesterase

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