SMTL ID : 5dyy.1

Crystal structure of human butyrylcholinesterase in complex with N-((1-benzylpiperidin-3-yl)methyl)naphthalene-2-sulfonamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 3 residues within 4Å: Chain A: D.55, I.56, N.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.56 Water bridges: A:N.58

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

NAG-NAG.2: 4 residues within 4Å: Chain A: K.106, N.107, N.189, K.191 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 11 residues within 4Å: Chain A: N.474, Y.478, N.480, N.482, E.483, T.484, Q.485 Chain B: C.67, D.88, L.89, Q.271 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.89, B:L.89

1 x NAG- FUL: beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUL.3: 4 residues within 4Å: Chain A: N.242, N.246, K.249, F.279 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.246, A:N.246, A:F.279 Hydrophobic interactions: A:N.246, A:K.249

2 x NAG- NAG- FUL: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUL.5: 4 residues within 4Å: Chain A: N.487, S.488, T.489, T.509 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.489, A:T.489 Water bridges: A:T.489 NAG-NAG-FUL.6: 7 residues within 4Å: Chain B: Y.238, N.242, N.246, L.250, F.279, P.282, Y.283 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.283

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: L.19, Y.62, W.99, D.130, K.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.99, A:D.130, A:K.132 GOL.8: 6 residues within 4Å: Chain A: N.229, Y.397, C.401, P.402, W.523, T.524 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.229 Water bridges: A:E.405 GOL.9: 6 residues within 4Å: Chain A: Y.34, S.49, L.50, L.174, Q.177, W.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.49, A:L.50 Water bridges: A:N.182 GOL.15: 5 residues within 4Å: Chain B: L.19, Y.62, W.99, D.130, K.132 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.99, B:K.132 GOL.16: 7 residues within 4Å: Chain B: H.78, M.82, S.426, K.428, L.429, P.430, E.444 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.78, B:S.426, B:S.426

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

EDO.10: 5 residues within 4Å: Chain A: H.78, M.82, K.428, P.430, E.444 No protein-ligand interaction detected (PLIP) EDO.17: 4 residues within 4Å: Chain B: R.43, R.266, K.268, P.270 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.43, B:K.268 Water bridges: B:G.40, B:E.91 EDO.18: 7 residues within 4Å: Chain B: P.231, W.232, V.234, T.235, E.239, R.243, V.289 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.289

2 x 5HH: N-{[(3R)-1-benzylpiperidin-3-yl]methyl}naphthalene-2-sulfonamide(Non-covalent)

5HH.11: 16 residues within 4Å: Chain A: W.83, G.117, G.118, Q.120, T.121, S.199, W.232, L.287, S.288, F.330, Y.333, F.399, W.431, M.438, H.439, Y.441 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.232, A:L.287, A:F.399, A:W.431, A:Y.441 Hydrogen bonds: A:T.121, A:T.121 Salt bridges: A:D.71 pi-Stacking: A:W.83, A:F.330 5HH.19: 15 residues within 4Å: Chain B: W.83, G.117, G.118, Q.120, T.121, S.199, W.232, L.287, S.288, F.330, Y.333, F.399, W.431, H.439, Y.441 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.232, B:L.287, B:F.330, B:F.399, B:W.431, B:Y.441 Salt bridges: B:D.71 pi-Stacking: B:W.83, B:F.330

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

CL.12: 3 residues within 4Å: Chain A: G.116, G.117, E.198 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: G.117, E.198 Ligand excluded by PLIP

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

NAG.13: 3 residues within 4Å: Chain A: I.5, N.18, T.25 No protein-ligand interaction detected (PLIP) NAG.14: 2 residues within 4Å: Chain A: S.339, N.342 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.342 Water bridges: A:G.337 NAG.21: 2 residues within 4Å: Chain B: N.18, T.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.18 NAG.22: 3 residues within 4Å: Chain B: R.15, I.56, N.58 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.58 NAG.23: 2 residues within 4Å: Chain B: N.107, N.189 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.107, B:N.189 NAG.24: 2 residues within 4Å: Chain B: N.257, E.260 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.257 NAG.25: 4 residues within 4Å: Chain B: G.337, S.339, N.342, N.343 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.337, B:S.339 Water bridges: B:G.337 NAG.26: 3 residues within 4Å: Chain B: R.454, D.455, N.456 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.456 NAG.27: 4 residues within 4Å: Chain B: Y.478, N.482, E.483, T.484 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.480, B:N.482

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kosak, U. et al., Development of an in-vivo active reversible butyrylcholinesterase inhibitor. Sci Rep (2016)

Release Date

2017-01-18

Peptides

Cholinesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cholinesterase

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