SMTL ID : 8am1.1

Human butyrylcholinesterase in complex with zinc and N,N,N-trimethyl-2-oxo-2-(2-(pyridin-2-ylmethylene)hydrazineyl)ethan-1-aminium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

monomer

Ligands

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.1: 7 residues within 4Å: Chain A: N.241, N.245, K.248, L.249, F.278, P.281, Y.282 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.248, A:L.249 NAG-NAG-FUC.2: 6 residues within 4Å: Chain A: P.335, G.336, S.338, N.341, N.342, I.344 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.336

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

NAG.3: 2 residues within 4Å: Chain A: R.14, N.57 No protein-ligand interaction detected (PLIP) NAG.4: 2 residues within 4Å: Chain A: N.106, N.188 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.188 NAG.5: 2 residues within 4Å: Chain A: N.256, E.259 No protein-ligand interaction detected (PLIP) NAG.6: 4 residues within 4Å: Chain A: R.465, K.469, E.482, N.485 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.465, A:K.469, A:E.482 Hydrogen bonds: A:R.465, A:N.485

1 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.7: 2 residues within 4Å: Chain A: A.516 Ligands: SO4.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.516

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: L.18, L.29, Y.61, W.98, D.129, K.131 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.98, A:K.131 Water bridges: A:D.129 GOL.9: 6 residues within 4Å: Chain A: V.136, E.137, R.138, R.465, K.469, K.476 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.136, A:R.138, A:R.465, A:K.469 GOL.10: 7 residues within 4Å: Chain A: H.77, M.81, S.425, K.427, Y.440, E.443, Y.456 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.425, A:K.427, A:E.443 Water bridges: A:H.77, A:H.126, A:K.427 GOL.11: 5 residues within 4Å: Chain A: W.231, T.234, R.242, L.286, V.288 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.242, A:R.242, A:L.286, A:V.288 Water bridges: A:L.286, A:S.287

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

CL.12: 2 residues within 4Å: Chain A: R.347, Q.351 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain A: Y.385 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: F.525 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: T.488, T.508 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain A: R.386 Ligand excluded by PLIP CL.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain A: T.457, K.458 Ligand excluded by PLIP

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

SO4.19: 3 residues within 4Å: Chain A: R.515, Q.518 Ligands: NH4.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.515, A:Q.518, A:Q.518 Salt bridges: A:R.515 SO4.20: 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:N.414, A:N.415

2 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.21: 1 residues within 4Å: Chain A: Y.420 No protein-ligand interaction detected (PLIP) ZN.22: 2 residues within 4Å: Ligands: LWL.23, LWL.24 No protein-ligand interaction detected (PLIP)

2 x LWL: N,N,N-trimethyl-2-oxo-2-(2-(pyridin-2-ylmethylene)hydrazineyl)ethan-1-aminium(Non-covalent)

LWL.23: 12 residues within 4Å: Chain A: D.70, G.116, G.117, T.120, S.198, W.231, L.286, V.288, F.329, F.398 Ligands: ZN.22, LWL.24 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.286, A:V.288, A:F.398 Water bridges: A:G.117 Salt bridges: A:D.70 pi-Stacking: A:W.231, A:W.231 LWL.24: 14 residues within 4Å: Chain A: W.82, G.116, G.117, Y.128, E.197, S.198, A.328, F.329, Y.332, W.430, M.437, H.438 Ligands: ZN.22, LWL.23 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.430 Water bridges: A:G.117 Salt bridges: A:E.197 pi-Cation interactions: A:W.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nachon, F. et al., Grid-Type Quaternary Metallosupramolecular Compounds Inhibit Human Cholinesterases through Dynamic Multivalent Interactions. Chembiochem (2022)

Release Date

2023-06-14

Peptides

Cholinesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cholinesterase

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