SMTL ID : 5dyt.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-FUC.1: 4 residues within 4Å: Chain A: R.15, D.55, I.56, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.3: 5 residues within 4Å: Chain A: N.242, N.246, K.249, F.279, P.282 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.246, A:K.249 Hydrogen bonds: A:F.279 NAG-NAG-FUC.5: 4 residues within 4Å: Chain A: N.487, S.488, T.489, T.509 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.509 Hydrogen bonds: A:N.487, A:T.489, A:T.489

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.2: 4 residues within 4Å: Chain A: K.106, N.107, N.189, K.191 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 10 residues within 4Å: Chain A: 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 NAG-NAG.6: 6 residues within 4Å: Chain B: Y.238, N.242, N.246, P.282, Y.283 Ligands: FUL.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.283

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

NAG-FUC.7: 3 residues within 4Å: Chain B: K.428, D.455, N.456 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.428, B:N.456

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

NAG.8: 3 residues within 4Å: Chain A: I.5, N.18, T.25 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.18 NAG.9: 2 residues within 4Å: Chain A: S.339, N.342 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.337 NAG.18: 2 residues within 4Å: Chain B: I.5, N.18 No protein-ligand interaction detected (PLIP) NAG.19: 2 residues within 4Å: Chain B: R.15, N.58 No protein-ligand interaction detected (PLIP) NAG.20: 2 residues within 4Å: Chain B: N.107, N.189 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.189 NAG.22: 2 residues within 4Å: Chain B: N.257, E.260 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.257 NAG.23: 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.24: 4 residues within 4Å: Chain B: Y.478, N.482, E.483, T.484 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.482

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

5HB.10: 18 residues within 4Å: Chain A: W.83, G.117, G.118, Q.120, T.121, S.199, W.232, L.287, S.288, A.329, F.330, Y.333, F.399, W.431, M.438, H.439, Y.441 Ligands: UNX.16 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.329, A:F.330, A:Y.333, A:F.399, A:W.431, A:Y.441 Hydrogen bonds: A:T.121 Salt bridges: A:D.71 pi-Stacking: A:W.83, A:W.232, A:W.232, A:F.330 5HB.25: 19 residues within 4Å: Chain B: W.83, G.117, G.118, Q.120, T.121, S.199, W.232, L.287, S.288, V.289, A.329, F.330, Y.333, F.399, W.431, M.438, H.439, Y.441 Ligands: UNX.32 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.232, B:V.289, B:A.329, B:F.330, B:Y.333, B:Y.333, B:F.399, B:W.431, B:Y.441 Hydrogen bonds: B:T.121 Salt bridges: B:D.71 pi-Stacking: B:W.83, B:F.330

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 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:K.132, A:K.132 GOL.12: 7 residues within 4Å: Chain A: N.229, Y.397, C.401, P.402, E.405, W.523, T.524 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.229 GOL.13: 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.26: 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.27: 8 residues within 4Å: Chain B: P.231, W.232, T.285, L.287, S.288, V.289, N.398 Ligands: EDO.29 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.285, B:V.289, B:N.398

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

EDO.14: 4 residues within 4Å: Chain A: H.78, M.82, K.428, E.444 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.428 EDO.28: 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.29: 8 residues within 4Å: Chain B: P.231, W.232, V.234, T.235, E.239, R.243, V.289 Ligands: GOL.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.231, B:V.289 EDO.30: 1 residues within 4Å: Chain B: N.456 No protein-ligand interaction detected (PLIP)

6 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.15: 5 residues within 4Å: Chain A: G.116, G.117, E.198 Ligands: UNX.16, UNX.17 No protein-ligand interaction detected (PLIP) UNX.16: 3 residues within 4Å: Ligands: 5HB.10, UNX.15, UNX.17 No protein-ligand interaction detected (PLIP) UNX.17: 5 residues within 4Å: Chain A: G.117, E.198, S.199 Ligands: UNX.15, UNX.16 No protein-ligand interaction detected (PLIP) UNX.31: 3 residues within 4Å: Chain B: E.198 Ligands: UNX.32, UNX.33 No protein-ligand interaction detected (PLIP) UNX.32: 4 residues within 4Å: Chain B: W.83 Ligands: 5HB.25, UNX.31, UNX.33 No protein-ligand interaction detected (PLIP) UNX.33: 6 residues within 4Å: Chain B: W.83, G.116, G.117, E.198 Ligands: UNX.31, UNX.32 No protein-ligand interaction detected (PLIP)

1 x FUL: beta-L-fucopyranose(Non-covalent)

FUL.21: 5 residues within 4Å: Chain B: L.250, F.279, P.282 Ligands: NAG-NAG.6, NAG-NAG.6 No protein-ligand interaction detected (PLIP)

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

PEG.34: 10 residues within 4Å: Chain B: H.78, M.82, H.127, V.128, S.426, K.428, L.429, P.430, E.444, Y.457 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.426, B:S.426, B:Y.457

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

2016-10-05

Peptides

Cholinesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cholinesterase

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