SMTL ID : 7q1n.1

Crystal structure of human butyrylcholinesterase in complex with N-[(2R)-3-[(cyclohexylmethyl)amino]-2-hydroxypropyl]-2,2-diphenylacetamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

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.3, R.14, N.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.14, A:N.57

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.2: 4 residues within 4Å: Chain A: N.106, N.188, K.190, S.191 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.188 Water bridges: A:T.108, A:T.108, A:T.108 NAG-NAG-FUC.3: 7 residues within 4Å: Chain A: Y.237, N.241, N.245, L.249, F.278, P.281, Y.282 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.249 Hydrogen bonds: A:F.278, A:Y.282 NAG-NAG-FUC.4: 6 residues within 4Å: Chain A: P.335, G.336, F.337, S.338, N.341, N.342 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.336

1 x 8IV: N-[(2R)-3-(cyclohexylmethylamino)-2-oxidanyl-propyl]-2,2-diphenyl-ethanamide(Non-covalent)

8IV.5: 18 residues within 4Å: Chain A: D.70, W.82, G.116, G.117, T.120, S.198, W.231, P.285, L.286, V.288, A.328, F.329, Y.332, F.398, W.430, M.437, H.438 Ligands: GOA.10 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.288, A:A.328, A:F.329, A:F.329, A:F.398, A:W.430 Hydrogen bonds: A:D.70 Water bridges: A:D.70 pi-Stacking: A:W.231, A:W.231, A:Y.332

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

NAG.6: 2 residues within 4Å: Chain A: N.256, T.258 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.258 NAG.7: 4 residues within 4Å: Chain A: R.465, K.469, E.482, N.485 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.469, A:E.482 Hydrogen bonds: A:R.465, A:N.485

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: W.231, T.234, E.238, R.242, L.286, S.287, V.288 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.231, A:E.238, A:R.242, A:R.242, A:S.287, A:V.288 Water bridges: A:V.233, A:T.234 GOL.9: 1 residues within 4Å: Chain A: D.340 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.339

1 x GOA: GLYCOLIC ACID(Non-covalent)

GOA.10: 4 residues within 4Å: Chain A: W.82, G.116, E.197 Ligands: 8IV.5 5 PLIP interactions: 5 interactions with chain A Water bridges: A:W.82, A:W.82, A:G.115, A:G.116 Salt bridges: A:H.438

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

SO4.11: 4 residues within 4Å: Chain A: Q.316, G.413, N.414, N.415 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.316, A:G.413, A:N.415 SO4.12: 3 residues within 4Å: Chain A: R.347, K.348, Q.351 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.351 Salt bridges: A:R.347, A:K.348 SO4.13: 4 residues within 4Å: Chain A: Q.486, S.487, T.488, T.508 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.470, A:T.488, A:T.488, A:T.508, A:T.508, A:T.508 Water bridges: A:Q.486, A:S.487

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

CL.14: 4 residues within 4Å: Chain A: M.81, Y.440, E.443 Ligands: CL.20 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: K.323, Y.420, R.515 Ligands: NA.28 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: R.515 Ligands: NA.28 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Ligands: CL.24 Ligand excluded by PLIP CL.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.19: 1 residues within 4Å: Chain A: Q.498 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain A: H.77, M.81 Ligands: CL.14 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain A: Y.385 Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain A: R.386 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain A: C.66, L.88, Q.270 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain A: F.371, H.372, F.521 Ligands: CL.17 Ligand excluded by PLIP CL.25: 1 residues within 4Å: Chain A: N.85 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain A: A.62, N.63 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.27: 1 residues within 4Å: Chain A: F.525 No protein-ligand interaction detected (PLIP) NA.28: 3 residues within 4Å: Chain A: R.515 Ligands: CL.15, CL.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.515

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Panek, D. et al., Discovery of new, highly potent and selective inhibitors of BuChE - design, synthesis, in vitro and in vivo evaluation and crystallography studies. Eur.J.Med.Chem. (2023)

Release Date

2022-11-16

Peptides

Cholinesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cholinesterase

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