SMTL ID : 7amz.1

Crystal structure of human Butyrylcholinesterase in complex with N-((2S,3R)-4-((2,2-dimethylpropyl)amino)-3-hydroxy-1-phenylbutan-2-yl)-2,2-diphenylacetamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 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: 6 residues within 4Å: Chain A: N.106, N.188, K.190, S.191, R.219, K.476 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.188, A:S.191, A:R.219 Water bridges: A:T.108, A:T.108 NAG-NAG-FUC.3: 7 residues within 4Å: Chain A: Y.237, N.241, N.245, K.248, L.249, F.278, P.281 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.281 Hydrogen bonds: A:K.248 NAG-NAG-FUC.4: 5 residues within 4Å: Chain A: P.335, G.336, S.338, N.341, N.342 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.338, A:G.336

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

NAG.5: 1 residues within 4Å: Chain A: N.256 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.256 NAG.6: 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

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: L.18, Y.61, W.98, D.129, K.131 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.98, A:D.129, A:K.131 GOL.8: 7 residues within 4Å: Chain A: H.77, M.81, V.127, K.427, Y.440, E.443, Y.456 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.126, A:K.427, A:K.427, A:E.443 GOL.9: 7 residues within 4Å: Chain A: W.231, T.234, E.238, R.242, L.286, S.287, V.288 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.231, A:E.238, A:R.242, A:R.242, A:L.286, A:V.288

1 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.10: 5 residues within 4Å: Chain A: F.76, K.339, D.340, P.429, P.431 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.339, A:K.339, A:D.340

1 x RNZ: 2,2-dimethylpropyl-[(2~{R},3~{S})-3-(2,2-diphenylethanoylamino)-2-oxidanyl-4-phenyl-butyl]azanium(Non-covalent)

RNZ.11: 18 residues within 4Å: Chain A: W.82, G.115, G.116, G.117, Q.119, T.120, Y.128, E.197, S.198, W.231, P.285, L.286, S.287, A.328, F.329, Y.332, F.398, H.438 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.82, A:Q.119, A:T.120, A:F.329, A:F.329, A:F.398 Hydrogen bonds: A:T.120 Water bridges: A:D.70, A:G.116 pi-Stacking: A:W.231, A:W.231, A:Y.332

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

MES.12: 5 residues within 4Å: Chain A: K.323, Y.420, L.514, R.515, Q.518 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.515, A:R.515, A:A.516 Salt bridges: A:K.323, A:R.515

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

SO4.13: 4 residues within 4Å: Chain A: Q.316, G.413, N.414, N.415 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.316, A:G.413, A:N.414, A:N.415 SO4.14: 5 residues within 4Å: Chain A: R.470, Q.486, S.487, T.488, T.508 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.470, A:S.487, A:T.488, A:T.488, A:T.508, A:T.508 Water bridges: A:S.466

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pasieka, A. et al., Discovery of multifunctional anti-Alzheimer's agents with a unique mechanism of action including inhibition of the enzyme butyrylcholinesterase and gamma-aminobutyric acid transporters. Eur.J.Med.Chem. (2021)

Release Date

2021-05-26

Peptides

Cholinesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cholinesterase

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