SMTL ID : 6g4p.1

Non-aged form of Torpedo californica acetylcholinesterase inhibited by tabun analog NEDPA bound to uncharged reactivator 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.83 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: M.16, N.59, S.61, T.62 No protein-ligand interaction detected (PLIP) NAG.2: 2 residues within 4Å: Chain A: G.415, N.416 No protein-ligand interaction detected (PLIP) NAG.9: 3 residues within 4Å: Chain B: N.59, S.61, T.62 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.59, B:S.61 NAG.10: 1 residues within 4Å: Chain B: N.416 No protein-ligand interaction detected (PLIP)

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

ELT.3: 11 residues within 4Å: Chain A: G.117, G.118, G.119, S.200, A.201, W.233, F.288, F.290, F.331, H.440 Ligands: PG4.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.118, A:G.119, A:A.201 ELT.11: 10 residues within 4Å: Chain B: G.118, G.119, S.200, A.201, W.233, F.288, F.290, F.331, H.440 Ligands: PG4.18 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.118, B:G.119, B:A.201

2 x JDS: 6-[4-[(7-chloranyl-1,2,3,4-tetrahydroacridin-9-yl)amino]butyl]-2-[(~{Z})-hydroxyiminomethyl]pyridin-3-ol(Non-covalent)

JDS.4: 9 residues within 4Å: Chain A: Y.70, Q.74, W.279, L.282, S.286, F.331, Y.334, G.335 Ligands: PG4.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.70, A:W.279, A:W.279, A:L.282 Hydrogen bonds: A:Y.70, A:Q.74 Water bridges: A:F.288 pi-Stacking: A:W.279 JDS.12: 6 residues within 4Å: Chain B: Y.70, Y.121, W.279, S.286, Y.334 Ligands: PG4.18 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.70, B:W.279, B:W.279, B:W.279, B:W.279, B:W.279 Hydrogen bonds: B:Y.70, B:W.279, B:S.286

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

CL.5: 1 residues within 4Å: Chain A: T.497 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: H.406, N.525 Ligand excluded by PLIP CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: N.481, N.483, K.491 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain B: E.139, H.471, T.475, K.478 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: T.459, E.461 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain B: R.289 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain B: L.23, Y.134 Ligand excluded by PLIP

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

PG4.8: 12 residues within 4Å: Chain A: W.84, G.117, G.118, Y.121, E.199, F.290, F.330, F.331, Y.334, H.440 Ligands: ELT.3, JDS.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.121, A:E.199 Water bridges: A:G.117 PG4.18: 10 residues within 4Å: Chain B: W.84, G.117, G.118, Y.121, F.330, F.331, Y.334, H.440 Ligands: ELT.11, JDS.12 No protein-ligand interaction detected (PLIP)

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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