SMTL ID : 6rua.1

Structure of recombinant human butyrylcholinesterase in complex with a coumarin-based fluorescent probe linked to sulfonamide type inhibitor.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: I.4, N.17, T.24 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: K.105, N.106, N.188, K.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.190, A:K.190 NAG-NAG.5: 6 residues within 4Å: Chain A: Y.477, N.479, N.481, E.482, T.483, Q.484 No protein-ligand interaction detected (PLIP)

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

NAG-FUC.2: 3 residues within 4Å: Chain A: R.14, I.55, N.57 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.14, A:I.55, A:N.57

1 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.4: 5 residues within 4Å: Chain A: N.241, N.245, K.248, F.278, P.281 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.245, A:K.248

4 x NAG- NAG- FUL: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUL.6: 6 residues within 4Å: Chain A: E.482, N.486, S.487, T.488, E.506, T.508 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.486, A:T.488, A:T.488 NAG-NAG-FUL.16: 6 residues within 4Å: Chain B: Y.237, N.241, N.245, K.248, L.249, F.278 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.245 NAG-NAG-FUL.17: 3 residues within 4Å: Chain B: E.255, N.256, E.259 No protein-ligand interaction detected (PLIP) NAG-NAG-FUL.18: 3 residues within 4Å: Chain B: K.427, D.454, N.455 No protein-ligand interaction detected (PLIP)

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

NAG.7: 2 residues within 4Å: Chain A: S.338, N.341 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.338, A:N.341 Water bridges: A:G.336, A:G.336 NAG.19: 1 residues within 4Å: Chain B: N.17 No protein-ligand interaction detected (PLIP) NAG.20: 2 residues within 4Å: Chain B: R.14, N.57 No protein-ligand interaction detected (PLIP) NAG.21: 3 residues within 4Å: Chain B: N.106, N.188, K.190 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.188 NAG.22: 5 residues within 4Å: Chain B: G.336, S.338, N.341, N.342, I.344 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.336 NAG.23: 3 residues within 4Å: Chain B: Y.477, N.481, E.482 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.481

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 4 residues within 4Å: Chain A: H.77, M.81, K.427, E.443 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.425, A:E.443 EDO.9: 3 residues within 4Å: Chain A: K.494, S.495, T.496 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.495, A:T.496 EDO.10: 2 residues within 4Å: Chain A: G.116, T.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.116 EDO.11: 6 residues within 4Å: Chain A: N.10, Y.33, S.48, L.49, Q.176, K.180 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.49 EDO.13: 4 residues within 4Å: Chain A: N.106, T.108, N.188, K.476 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.106, A:T.108, A:N.188, A:K.476 EDO.15: 4 residues within 4Å: Chain A: N.228, C.400, P.401, T.523 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.228, A:C.400 EDO.25: 6 residues within 4Å: Chain A: F.525 Chain B: S.368, F.371, H.372, F.521, F.525 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.368, B:H.372 Water bridges: A:H.372 EDO.26: 5 residues within 4Å: Chain B: T.284, L.286, F.357, Y.396, N.397 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.286 EDO.27: 7 residues within 4Å: Chain B: Q.35, P.37, L.41, K.44, K.45, P.46, Q.47 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.35, B:Q.35, B:K.44, B:Q.47, B:R.147

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

CL.12: 1 residues within 4Å: Chain A: R.386 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: G.116, E.197 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain B: R.242 Ligand excluded by PLIP CL.30: 1 residues within 4Å: Chain B: E.197 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain B: R.42, K.267, P.269 Ligand excluded by PLIP

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

PEG.24: 10 residues within 4Å: Chain B: H.77, M.81, H.126, V.127, S.425, K.427, L.428, P.429, E.443, Y.456 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.425, B:S.425

1 x KJT: diethyl-[6-[[2-[2-[2-[naphthalen-2-ylsulfonyl-[[(3~{R})-1-(phenylmethyl)piperidin-3-yl]methyl]amino]ethoxy]ethoxy]ethylamino]-oxidanyl-methyl]-7-oxidanylidene-1,3,4,4~{a},5,6,8,8~{a}-octahydronaphthalen-2-ylidene]azanium(Non-covalent)

KJT.29: 17 residues within 4Å: Chain B: W.82, G.116, G.117, Q.119, T.120, S.198, W.231, L.286, S.287, A.328, F.329, Y.332, F.398, W.430, M.437, H.438, Y.440 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.328, B:F.329, B:Y.332, B:Y.332, B:F.398, B:W.430, B:Y.440 pi-Stacking: B:W.82, B:W.231, B:W.231, B:F.329

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.32: 14 residues within 4Å: Chain B: K.323, D.324, E.325, G.326, T.327, L.330, R.386, E.387, G.390, D.391, G.394, D.395, I.399, R.515 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.324, B:G.326, B:G.390, B:R.515

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pajk, S. et al., Development of potent reversible selective inhibitors of butyrylcholinesterase as fluorescent probes. J Enzyme Inhib Med Chem (2020)

Release Date

2020-01-22

Peptides

Cholinesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cholinesterase

Related Entries With Identical Sequence