SMTL ID : 5k5e.1

Discovery and Structure-Activity Relationships of a Highly Selective Butyrylcholinesterase Inhibitor by Structure-Based Virtual Screening

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

3 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.106, N.188, K.190 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.473, Y.477, N.481, E.482, Q.484 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.477 NAG-NAG.9: 6 residues within 4Å: Chain B: P.335, G.336, F.337, S.338, N.341, N.342 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.336

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

NAG.3: 3 residues within 4Å: Chain A: I.4, N.17, T.24 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.4 Hydrogen bonds: A:N.17, A:T.24 NAG.4: 2 residues within 4Å: Chain A: R.14, N.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.57, A:N.57 NAG.5: 3 residues within 4Å: Chain A: E.238, N.241, N.245 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.241, A:N.245 NAG.6: 2 residues within 4Å: Chain A: S.338, N.341 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.338, A:N.341 Water bridges: A:G.336 NAG.10: 3 residues within 4Å: Chain B: I.4, N.17, T.24 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.4 Hydrogen bonds: B:N.17 NAG.11: 2 residues within 4Å: Chain B: R.14, N.57 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.14 NAG.12: 2 residues within 4Å: Chain B: N.106, N.188 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.188 NAG.13: 3 residues within 4Å: Chain B: N.241, N.245, P.281 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.245 NAG.14: 1 residues within 4Å: Chain B: N.256 No protein-ligand interaction detected (PLIP) NAG.15: 4 residues within 4Å: Chain B: Y.477, N.481, E.482, T.483 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.483

2 x 6QS: [(2~{R})-oxolan-2-yl]methyl 4-(9-ethylcarbazol-3-yl)-2-methyl-5-oxidanylidene-4,6,7,8-tetrahydro-1~{H}-quinoline-3-carboxylate(Non-covalent)

6QS.7: 17 residues within 4Å: Chain A: W.82, G.115, G.116, G.117, Y.128, E.197, S.198, W.231, P.285, L.286, S.287, A.328, F.329, Y.332, F.398, H.438, G.439 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.82, A:A.328, A:F.329, A:F.329, A:F.398 Hydrogen bonds: A:H.438 pi-Stacking: A:W.82, A:W.82, A:W.231, A:W.231 6QS.16: 18 residues within 4Å: Chain B: W.82, G.115, G.116, G.117, T.120, Y.128, E.197, S.198, P.285, L.286, S.287, V.288, A.328, F.329, Y.332, F.398, H.438, G.439 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.82, B:W.82, B:V.288, B:A.328, B:F.329, B:F.329, B:F.398 Hydrogen bonds: B:T.120, B:H.438 pi-Stacking: B:W.82, B:W.231, B:W.231

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

EDO.8: 5 residues within 4Å: Chain A: Y.396, C.400, P.401, W.522, T.523 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.396 EDO.17: 4 residues within 4Å: Chain B: H.77, M.81, K.427, E.443 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.427 EDO.18: 3 residues within 4Å: Chain B: N.245, L.249, F.278 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 4 residues within 4Å: Chain B: Y.61, W.98, D.129, K.131 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.98, B:K.131, B:K.131 GOL.20: 3 residues within 4Å: Chain B: K.248, G.251, S.253 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dighe, S.N. et al., Discovery and Structure-Activity Relationships of a Highly Selective Butyrylcholinesterase Inhibitor by Structure-Based Virtual Screening. J.Med.Chem. (2016)

Release Date

2016-07-27

Peptides

Cholinesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cholinesterase

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