MolNFT v1 · #117125 · protein
Crystal structure of human butyrylcholinesterase in complex with N- ((1-benzylpiperidin-3-YL)METHYL)-N-(2-METHOXYETHYL)NAPHTHALENE-2- sulfonamide
5DYW: “Crystal structure of human butyrylcholinesterase in complex with N…”. X-ray diffraction, 5 ligands (5HF, NAG, FUL), 11 pockets (best druggability 0.80). MolNFT v1 #117125 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DYW
- 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
- 5HF, NAG, FUL, FUC, CL
- Pockets
- 11 · 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 | 37% helix, 17% strand | P06276 |
| B | Cholinesterase (EC 3.1.1.8) | protein | 525 | 36% helix, 17% strand | P06276 |
Ligands and binding sites
- 5HF · N-{[(3S)-1-benzylpiperidin-3-yl]methyl}-N-(2-methoxyethyl)naphthalene-2-sulfonamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B
- FUL · beta-L-fucopyranose · sugar · 4 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.80 | 0.82 | 82 | NAG, EDO, 5HF, CL |
| 2 | 575 | 0.77 | 0.83 | 46 | 5HF, CL |
| 3 | 452 | 0.64 | 0.77 | 42 | GOL |
| 4 | 248 | 0.56 | 0.77 | 28 | GOL, CL |
| 5 | 139 | 0.44 | 0.76 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 754 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 6 disulfide (N-glycosylation, disulfide).
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 5DYW · PDBe 5DYW · UniProt P06276
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