MolNFT v1 · #125829 · protein
Human butyrylcholinesterase complexed with N-propargyliperidines
5LKR: “Human butyrylcholinesterase complexed with N-propargyliperidines”. X-ray diffraction, 4 ligands (6YC, NAG, FUL), 11 pockets (best druggability 0.80). MolNFT v1 #125829 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5LKR
- Type
- protein
- Length
- 1,051 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
- 6YC, NAG, FUL, FUC
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cholinesterase (EC 3.1.1.8) | protein | 527 | 35% helix, 17% strand | P06276 |
| B | Cholinesterase (EC 3.1.1.8) | protein | 524 | 35% helix, 17% strand | P06276 |
Ligands and binding sites
- 6YC · ~{N}-(2-methoxyethyl)-~{N}-[[(3~{S})-1-prop-2-ynylpiperidin-3-yl]methyl]naphthalene-2-carboxamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B
- FUL · beta-L-fucopyranose · sugar · 2 copies · chains B, A
- FUC · alpha-L-fucopyranose · sugar · chains A
- GOL · Glycerol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · 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 | 1139 | 0.80 | 0.81 | 88 | NAG, 6YC |
| 2 | 592 | 0.77 | 0.83 | 47 | 6YC |
| 3 | 215 | 0.56 | 0.78 | 26 | empty |
| 4 | 242 | 0.54 | 0.77 | 27 | empty |
| 5 | 172 | 0.46 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 698 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 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 5LKR · PDBe 5LKR · UniProt P06276
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