SMTL ID : 7q1p.1

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

Coordinates

PDB Format Compare

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: 6 residues within 4Å: Chain A: N.106, N.188, K.190, S.191, R.219, K.476 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.188, A:S.191, A:R.219, A:N.188 Water bridges: A:S.191

2 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: 7 residues within 4Å: Chain A: Y.237, N.241, N.245, L.249, F.278, V.280, P.281 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.245 Hydrogen bonds: A:F.278, A:V.280 NAG-NAG-FUC.3: 7 residues within 4Å: Chain A: P.335, G.336, S.338, D.340, N.341, N.342, I.344 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

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 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.8: 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:R.242, A:S.287, A:V.288 Water bridges: A:W.231 GOL.10: 9 residues within 4Å: Chain A: H.77, M.81, V.127, S.425, K.427, L.428, P.429, Y.440, E.443 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.126, A:S.425 Water bridges: A:H.77, A:Y.456, A:Y.456 GOL.11: 3 residues within 4Å: Chain A: Y.456, T.457, K.458 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.458

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

8UW.9: 19 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, Y.440 Ligands: GOA.12 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:W.82, A:V.288, A:A.328, A:F.329, A:F.329, A:Y.332, A:F.398, A:W.430, A:Y.440 Hydrogen bonds: A:D.70, A:D.70, A:Y.332 Water bridges: A:Y.332, A:Y.332 pi-Stacking: A:W.231, A:W.231, A:F.329, A:Y.332

1 x GOA: GLYCOLIC ACID(Non-covalent)

GOA.12: 6 residues within 4Å: Chain A: G.115, G.116, E.197, S.198, H.438 Ligands: 8UW.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.115 Water bridges: A:A.199 Salt bridges: A:H.438

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

SO4.13: 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 SO4.14: 4 residues within 4Å: Chain A: R.40, K.262, R.265, N.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.266 Salt bridges: A:K.262 SO4.15: 3 residues within 4Å: Chain A: R.347, Q.351, E.367 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.351, A:E.367 Salt bridges: A:R.347

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

NA.16: 3 residues within 4Å: Chain A: R.515 Ligands: CL.20, CL.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.515

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

CL.17: 1 residues within 4Å: Chain A: R.386 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain A: F.371, H.372 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain A: W.376, Y.385 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain A: Y.420, R.515 Ligands: NA.16 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain A: R.515 Ligands: NA.16 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain A: S.487, T.488, T.508 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain A: P.431, E.432 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain A: L.236 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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