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Crystal structure of human butyrylcholinesterase in complex with N- ((1-benzylpiperidin-3-YL)METHYL)NAPHTHALENE-2-sulfonamide
Analyse Crystal structure of human butyrylcholinesterase in complex with N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DYY
- Type
- protein
- Length
- 1,052 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholinesterase
- EC
- 3.1.1.8
- UniProt
- P06276
- Ligands
- 5HH, NAG, FUL, FUC, CL
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cholinesterase (EC 3.1.1.8) | protein | 527 | 36% helix, 18% strand | P06276 |
| B | Cholinesterase (EC 3.1.1.8) | protein | 525 | 36% helix, 17% strand | P06276 |
Ligands and binding sites
- 5HH · N-{[(3R)-1-benzylpiperidin-3-yl]methyl}naphthalene-2-sulfonamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B
- FUL · beta-L-fucopyranose · sugar · 3 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.80 | 0.81 | 78 | NAG, 5HH, CL |
| 2 | 541 | 0.78 | 0.85 | 44 | 5HH, CL |
| 3 | 404 | 0.60 | 0.76 | 46 | EDO |
| 4 | 241 | 0.53 | 0.76 | 25 | empty |
| 5 | 79 | 0.50 | 0.83 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 725 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 6 disulfide, 2 modified (N-glycosylation, disulfide, oxidation).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P06276
- Elsewhere: RCSB PDB 5DYY · PDBe 5DYY · UniProt P06276
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