SMTL ID : 7q1o.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

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: 5 residues within 4Å: Chain A: N.106, N.188, K.190, S.191, R.219 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.2: 7 residues within 4Å: Chain A: N.241, N.245, K.248, L.249, F.278, V.280, P.281 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.245, A:L.249 Hydrogen bonds: A:K.248, A:F.278, A:V.280 NAG-NAG-FUC.3: 6 residues within 4Å: Chain A: P.335, G.336, S.338, D.340, N.341, N.342 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.340 Hydrogen bonds: A:S.338, A:G.336

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

NAG.4: 2 residues within 4Å: Chain A: R.14, N.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.14, A:N.57 NAG.5: 1 residues within 4Å: Chain A: N.256 No protein-ligand interaction detected (PLIP) 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: 7 residues within 4Å: Chain A: W.231, V.233, T.234, E.238, R.242, S.287, V.288 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.231, A:R.242, A:R.242, A:V.288 GOL.9: 6 residues within 4Å: Chain A: L.18, L.29, Y.61, W.98, D.129, K.131 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.98, A:K.131, A:K.131 Water bridges: A:D.129 GOL.10: 2 residues within 4Å: Chain A: N.85, H.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.85, A:H.126

1 x 9CI: N-[(2S)-3-(cyclohexylmethylamino)-2-oxidanyl-propyl]-3,3-diphenyl-propanamide(Non-covalent)

9CI.8: 18 residues within 4Å: Chain A: D.70, W.82, G.116, G.117, T.120, S.198, W.231, L.286, V.288, A.328, F.329, Y.332, F.398, W.430, M.437, H.438, Y.440 Ligands: GOA.11 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.231, A:L.286, A:V.288, A:A.328, A:Y.332, A:F.398, A:W.430, A:Y.440 Hydrogen bonds: A:D.70 Water bridges: A:D.70 pi-Stacking: A:W.231, A:W.231, A:F.329, A:F.329, A:Y.332

1 x GOA: GLYCOLIC ACID(Non-covalent)

GOA.11: 6 residues within 4Å: Chain A: G.115, G.116, E.197, S.198, H.438 Ligands: 9CI.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.115 Water bridges: A:W.82, A:A.199 Salt bridges: A:H.438

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

SO4.12: 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:N.414, A:N.415, A:N.415 SO4.13: 4 residues within 4Å: Chain A: Q.486, S.487, T.488, T.508 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.470, A:Q.486, A:T.488, A:T.488, A:T.508 SO4.14: 5 residues within 4Å: Chain A: L.514, R.515, Q.518 Ligands: SO4.15, NA.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.515, A:Q.518 Salt bridges: A:R.515 SO4.15: 5 residues within 4Å: Chain A: K.323, Y.420, R.515 Ligands: SO4.14, NA.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.420 Salt bridges: A:K.323, A:R.515 SO4.16: 2 residues within 4Å: Chain A: T.457, K.458 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.458 SO4.17: 2 residues within 4Å: Chain A: R.347, Q.351 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.351 Salt bridges: A:R.347

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

NA.18: 3 residues within 4Å: Chain A: Y.500 Ligands: SO4.14, SO4.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.500, A:Y.500

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

CL.19: 2 residues within 4Å: Chain A: W.376, Y.385 Ligand excluded by PLIP

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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