SMTL ID : 5nn0.1

Crystal structure of huBChE with N-((1-(2,3-dihydro-1H-inden-2-yl)piperidin-3-yl)methyl)-N-(2-(dimethylamino)ethyl)-2-naphthamide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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: 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 NAG-NAG-FUC.3: 7 residues within 4Å: Chain A: E.238, N.241, N.245, L.249, F.278, V.280, P.281 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.245, A:L.249 Hydrogen bonds: A:V.280 Water bridges: A:F.278

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.2: 6 residues within 4Å: Chain A: N.106, N.188, K.190, S.191, R.219, K.476 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.188, A:S.191, A:R.219, A:N.188, A:K.190 Water bridges: A:T.108, A:T.108, A:T.108, A:R.219 Hydrophobic interactions: A:N.106

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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.57 NAG.5: 4 residues within 4Å: Chain A: R.465, K.469, N.485 Ligands: SO4.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.469 Hydrogen bonds: A:R.465, A:N.485 Water bridges: A:S.466 NAG.6: 1 residues within 4Å: Chain A: N.256 No protein-ligand interaction detected (PLIP)

2 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.98, A:K.131 Water bridges: A:D.129 GOL.8: 4 residues within 4Å: Chain A: N.85, L.125, H.126 Ligands: 1PG.23 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.85, A:H.126 Water bridges: A:M.81, A:V.127

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

SO4.9: 6 residues within 4Å: Chain A: L.208, L.209, S.210, H.214, F.312, K.313 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.210 Water bridges: A:F.312, A:F.312 Salt bridges: A:H.214 SO4.10: 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 Water bridges: A:N.415 SO4.11: 4 residues within 4Å: Chain A: W.231, R.242, S.287, V.288 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.231, A:V.288 Water bridges: A:R.242, A:R.242 Salt bridges: A:R.242 SO4.12: 1 residues within 4Å: Chain A: R.135 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.135 SO4.13: 2 residues within 4Å: Chain A: R.465 Ligands: NAG.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.465 SO4.14: 5 residues within 4Å: Chain A: R.470, N.486, S.487, T.488, T.508 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.470, A:S.487, A:T.488, A:T.488, A:T.508, A:T.508 SO4.15: 3 residues within 4Å: Chain A: S.368, H.372, F.525 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.372

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

CL.16: 1 residues within 4Å: Chain A: T.512 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain A: R.265 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain A: R.347, Q.351 Ligand excluded by PLIP

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

MES.19: 5 residues within 4Å: Chain A: H.372, Y.373, Q.517, Q.518, F.521 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.372, A:Q.517, A:Q.518 MES.20: 6 residues within 4Å: Chain A: K.323, Y.420, Y.500, L.514, R.515, Q.518 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.515, A:R.515 Water bridges: A:K.323, A:Y.500 Salt bridges: A:K.323, A:R.515

2 x 92H: ~{N}-[[(3~{R})-1-(2,3-dihydro-1~{H}-inden-2-yl)piperidin-3-yl]methyl]-~{N}-[2-(dimethylamino)ethyl]naphthalene-2-carboxamide(Non-covalent)

92H.21: 6 residues within 4Å: Chain A: L.236, Y.237, V.294, G.296, T.300, M.302 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.236, A:V.294 92H.22: 16 residues within 4Å: Chain A: N.68, I.69, D.70, W.82, G.116, G.117, T.120, E.197, W.231, L.286, S.287, V.288, F.329, Y.332, F.398, G.439 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:D.70, A:T.120, A:L.286, A:V.288, A:F.329, A:F.329, A:Y.332, A:F.398 Hydrogen bonds: A:G.117 Water bridges: A:G.116, A:G.116 Salt bridges: A:D.70, A:E.197 pi-Stacking: A:W.231, A:W.231 pi-Cation interactions: A:W.82, A:W.82

1 x 1PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL(Non-covalent)

1PG.23: 13 residues within 4Å: Chain A: G.75, F.76, H.77, E.80, M.81, H.126, V.127, S.425, K.427, L.428, Y.440, E.443 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.75, A:E.80, A:H.126 Water bridges: A:H.126

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.24: 4 residues within 4Å: Chain A: R.219, T.315, Q.316, Y.477 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.218, A:R.219, A:Q.316, A:Y.477 Water bridges: A:R.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kosak, U. et al., The Magic of Crystal Structure-Based Inhibitor Optimization: Development of a Butyrylcholinesterase Inhibitor with Picomolar Affinity and in Vivo Activity. J. Med. Chem. (2018)

Release Date

2018-03-14

Peptides

Cholinesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cholinesterase

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