SMTL ID : 6h12.1

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)methoxy)methyl)pyridin-2-yl)urea

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

MES.1: 5 residues within 4Å: Chain A: G.41, N.42, H.264, R.267, E.268 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.267 MES.11: 9 residues within 4Å: Chain A: S.108, T.109, T.110, E.139, E.140, V.141, D.190, T.193, K.478 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.109, A:T.110, A:T.110, A:T.110, A:D.190 MES.12: 4 residues within 4Å: Chain A: N.481, N.483, P.485, K.491 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.481, A:N.483 MES.14: 5 residues within 4Å: Chain A: R.242, R.243, V.246, L.256, D.259 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.259 Salt bridges: A:R.242

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: N.424, H.425, N.506, T.507, E.508 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.424, A:H.425, A:T.507 GOL.9: 7 residues within 4Å: Chain A: P.232, R.244, P.283, F.284, R.289, H.362 Ligands: PGE.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.244 Water bridges: A:R.244, A:F.290 GOL.31: 3 residues within 4Å: Chain B: S.108, D.190, T.193 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.193, B:T.193

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

PGE.3: 4 residues within 4Å: Chain A: E.240, R.244, P.283 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.244 PGE.32: 3 residues within 4Å: Chain B: R.216, D.217, K.315 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.216 Water bridges: B:K.315, B:K.316

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

EDO.4: 1 residues within 4Å: Chain A: Q.500 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.500 EDO.5: 5 residues within 4Å: Chain A: H.425, T.459, E.461, E.462, T.507 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.459, A:E.461, A:T.507, A:T.507 EDO.6: 1 residues within 4Å: Chain A: K.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.107 EDO.7: 3 residues within 4Å: Chain A: F.75, F.78, P.433 No protein-ligand interaction detected (PLIP) EDO.8: 4 residues within 4Å: Chain A: L.430, V.431, W.432, P.433 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.430 Water bridges: A:E.434 EDO.10: 4 residues within 4Å: Chain A: H.398, P.403, W.524, P.529 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.398, A:H.398 EDO.28: 2 residues within 4Å: Chain B: N.230, S.235 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.235 Water bridges: B:S.235, B:S.235 EDO.29: 2 residues within 4Å: Chain B: Q.500, V.518 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.500 EDO.30: 5 residues within 4Å: Chain B: T.109, E.139, E.140, A.474, K.478 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.109, B:T.109 Water bridges: B:T.110, B:T.475, B:K.478 EDO.33: 3 residues within 4Å: Chain B: F.75, F.78 Ligands: PEG.41 No protein-ligand interaction detected (PLIP) EDO.34: 6 residues within 4Å: Chain A: V.522, Q.526, F.527 Chain B: D.369, L.373, W.378 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.378 EDO.36: 3 residues within 4Å: Chain B: V.57, W.58, N.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.57, B:N.59 EDO.37: 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:R.267

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

SO4.13: 6 residues within 4Å: Chain A: P.21, V.22, L.23, K.133, Y.134, E.455 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.23, A:Y.134 Salt bridges: A:K.133 SO4.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.35: 6 residues within 4Å: Chain B: P.21, V.22, L.23, K.133, Y.134, E.455 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.23 Salt bridges: B:K.133

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

PEG.15: 6 residues within 4Å: Chain A: K.325, D.326, D.389, D.393, F.422, R.517 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.517 PEG.16: 2 residues within 4Å: Chain A: N.230, S.235 5 PLIP interactions: 5 interactions with chain A Water bridges: A:S.235, A:S.235, A:S.237, A:S.237, A:L.305 PEG.17: 4 residues within 4Å: Chain A: R.220, R.221, Q.318, T.479 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.220, A:R.221, A:Q.318, A:Q.318 Water bridges: A:R.221 PEG.18: 2 residues within 4Å: Chain A: R.216, D.217 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.216 PEG.38: 6 residues within 4Å: Chain B: R.242, V.246, L.256, S.258, D.259, L.262 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.242, B:D.259 PEG.39: 2 residues within 4Å: Chain B: I.296, D.297 No protein-ligand interaction detected (PLIP) PEG.40: 3 residues within 4Å: Chain B: E.306, S.307, N.310 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.310 PEG.41: 3 residues within 4Å: Chain B: L.333, F.339 Ligands: EDO.33 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.339

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

NAG.19: 3 residues within 4Å: Chain A: N.59, S.61, T.62 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.61 NAG.20: 2 residues within 4Å: Chain A: G.415, N.416 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.416 Water bridges: A:N.416, A:N.416 NAG.42: 3 residues within 4Å: Chain B: N.59, S.61, T.62 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.61 NAG.43: 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.44: 2 residues within 4Å: Chain B: E.455, N.457 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.455

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

CL.21: 1 residues within 4Å: Chain A: W.435 Ligand excluded by PLIP CL.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain A: K.454, E.463 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain A: R.468 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain A: R.44, K.269 Ligand excluded by PLIP CL.45: 2 residues within 4Å: Chain B: R.44, K.269 Ligand excluded by PLIP

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

FJK.26: 13 residues within 4Å: Chain A: Y.70, Q.74, W.84, Y.121, E.199, W.279, F.330, F.331, Y.334, W.432, I.439, H.440, Y.442 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.84, A:W.279, A:F.330, A:W.432, A:I.439, A:Y.442 Water bridges: A:W.84, A:S.286, A:R.289 pi-Stacking: A:W.84, A:W.84, A:W.84, A:W.279, A:F.330, A:F.330 FJK.46: 15 residues within 4Å: Chain B: W.84, Y.121, E.199, W.279, L.282, F.284, D.285, S.286, F.330, F.331, G.335, W.432, I.439, H.440, Y.442 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:W.84, B:L.282, B:D.285, B:F.330, B:W.432, B:I.439, B:Y.442 Hydrogen bonds: B:Y.121, B:S.286 Water bridges: B:W.84, B:S.286, B:R.289 pi-Stacking: B:W.84, B:W.84, B:W.84, B:Y.121, B:W.279, B:F.330, B:F.330

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
A

B
B

Acetylcholinesterase

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