MolNFT v1 · #117122 · protein
Crystal structure of human butyrylcholinesterase in complex with N- ((1-benzylpiperidin-3-YL)METHYL)-N-methylnaphthalene-2-sulfonamide
5DYT: “Crystal structure of human butyrylcholinesterase in complex with N…”. X-ray diffraction, 5 ligands (5HB, NAG, FUC), 10 pockets (best druggability 0.80). MolNFT v1 #117122 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DYT
- 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
- 5HB, NAG, FUC, FUL, UNX
- Pockets
- 10 · 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
- 5HB · N-{[(3R)-1-benzylpiperidin-3-yl]methyl}-N-methylnaphthalene-2-sulfonamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B
- FUL · beta-L-fucopyranose · sugar · chains B
- UNX · Unknown atom or ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.80 | 0.82 | 82 | NAG, 5HB, UNX |
| 2 | 534 | 0.78 | 0.85 | 43 | 5HB, UNX |
| 3 | 355 | 0.59 | 0.76 | 42 | GOL, EDO |
| 4 | 360 | 0.59 | 0.76 | 39 | GOL |
| 5 | 66 | 0.45 | 0.83 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 728 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 5DYT · PDBe 5DYT · UniProt P06276
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