SMTL ID : 6h14.1

Crystal structure of TcACHE complexed to 1-(6-oxo-1,2,3,4,6,10b-hexahydropyrido[2,1-a]isoindol-10-yl)-3-(4-(1-(2-((1,2,3,4-tetrahydroacridin-9-yl)amino)ethyl)-1H-1,2,3-triazol-4-yl)pyridin-2-yl)urea

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.59, S.61, T.62 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: N.416, L.494 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.494 Hydrogen bonds: A:N.416 Water bridges: A:N.416, A:N.416 NAG.3: 2 residues within 4Å: Chain A: E.455, N.457 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.455, A:N.457 NAG.13: 3 residues within 4Å: Chain B: N.59, S.61, T.62 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.59, B:S.61, B:T.62 NAG.14: 3 residues within 4Å: Chain B: G.415, N.416, G.417 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.416 Water bridges: B:N.416, B:N.416 NAG.15: 1 residues within 4Å: Chain B: N.457 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.457

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

EDO.4: 5 residues within 4Å: Chain A: H.425, T.459, E.461, E.462, T.507 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.459, A:T.459, A:T.507 EDO.6: 4 residues within 4Å: Chain A: V.57, W.58, N.59 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.57, A:W.58, A:N.59 EDO.7: 5 residues within 4Å: Chain A: W.54, S.55, V.57, W.58 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.57 EDO.12: 3 residues within 4Å: Chain A: T.412, T.496, T.497 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.497 Water bridges: A:K.413, A:T.497, A:T.497, A:K.498 EDO.16: 2 residues within 4Å: Chain B: Q.500, V.518 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.500 EDO.17: 5 residues within 4Å: Chain A: Q.519 Chain B: Q.374, Y.375, T.376, D.377 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.375, B:Y.375, B:D.377 EDO.20: 4 residues within 4Å: Chain B: G.41, N.42, R.267, E.268 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.42 EDO.21: 3 residues within 4Å: Chain B: S.55, V.57, W.58 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: M.405, H.406, N.409, C.521, N.525 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.406, A:N.525 Water bridges: A:L.516, A:C.521 GOL.19: 6 residues within 4Å: Chain B: M.405, H.406, N.409, C.521, N.525, Q.526 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.406, B:N.525, B:Q.526 Water bridges: B:L.516, B:C.521

2 x FW8: 1-[(10~{b}~{S})-6-oxidanylidene-2,3,4,10~{b}-tetrahydro-1~{H}-pyrido[2,1-a]isoindol-10-yl]-3-[4-[1-[2-(1,2,3,4-tetrahydroacridin-9-ylamino)ethyl]-1,2,3-triazol-4-yl]pyridin-2-yl]urea(Non-covalent)

FW8.8: 19 residues within 4Å: Chain A: Y.70, G.80, W.84, Y.121, E.199, W.279, L.282, F.284, D.285, F.288, F.290, F.330, F.331, Y.334, W.432, I.439, H.440, G.441, Y.442 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:W.84, A:W.84, A:W.279, A:W.279, A:W.279, A:L.282, A:F.290, A:F.330, A:F.331, A:W.432, A:I.439, A:Y.442 Hydrogen bonds: A:Y.121, A:F.288 Water bridges: A:S.81, A:R.289, A:R.289 pi-Stacking: A:W.84, A:W.84, A:Y.121, A:W.279, A:F.330, A:F.330, A:F.330 FW8.22: 18 residues within 4Å: Chain B: Y.70, W.84, Y.121, E.199, W.279, L.282, F.284, S.286, F.288, F.290, F.330, F.331, Y.334, W.432, I.439, H.440, G.441, Y.442 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:W.84, B:W.84, B:W.279, B:W.279, B:W.279, B:L.282, B:F.290, B:F.330, B:F.331, B:W.432, B:I.439, B:Y.442 Hydrogen bonds: B:F.288 Water bridges: B:S.81, B:R.289, B:R.289 pi-Stacking: B:W.84, B:W.84, B:Y.121, B:W.279, B:F.330, B:F.330, B:F.330, B:Y.334

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

CL.9: 1 residues within 4Å: Chain A: W.435 Ligand excluded by PLIP

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.10: 5 residues within 4Å: Chain A: S.79, E.82, M.83, N.429, V.431 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.79, A:N.429 Water bridges: A:Y.458 PGE.23: 6 residues within 4Å: Chain B: S.79, E.82, M.83, D.128, N.429, V.431 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.79, B:D.128, B:N.429

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.11: 3 residues within 4Å: Chain A: N.481, N.483, K.491 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.481, A:N.483

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.18: 3 residues within 4Å: Chain B: V.238, I.296, G.298 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.304, B:S.304

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.24: 8 residues within 4Å: Chain B: K.325, D.326, R.388, D.389, D.392, E.434, W.435, G.437 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.388, B:D.392, B:D.392 Water bridges: B:D.326, B:R.388, B:G.437 Salt bridges: B:K.325

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oukoloff, K. et al., Design, biological evaluation and X-ray crystallography of nanomolar multifunctional ligands targeting simultaneously acetylcholinesterase and glycogen synthase kinase-3. Eur.J.Med.Chem. (2019)

Release Date

2019-05-15

Peptides

Acetylcholinesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Acetylcholinesterase

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