MolNFT v1 · #106769 · protein
Human butyrylcholinesterase in complex with N-((1-(2,3-dihydro-1H- inden-2-YL)PIPERIDIN-3-YL)METHYL)-N-(2-methoxyethyl)-2-naphthamide
4TPK: “Human butyrylcholinesterase in complex with N-((1-(2,3-dihydro-1H…”. X-ray diffraction, 4 ligands (3F9, NAG, FUL), 10 pockets (best druggability 0.79). MolNFT v1 #106769 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4TPK
- 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
- 3F9, NAG, FUL, FUC
- Pockets
- 10 · best druggability 0.79
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, 17% strand | P06276 |
| B | Cholinesterase (EC 3.1.1.8) | protein | 524 | 37% helix, 17% strand | P06276 |
Ligands and binding sites
- 3F9 · N-{[(3R)-1-(2,3-dihydro-1H-inden-2-yl)piperidin-3-yl]methyl}-N-(2-methoxyethyl)naphthalene-2-carboxamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B
- FUL · beta-L-fucopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- 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
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 | 1116 | 0.79 | 0.81 | 80 | NAG, 3F9, GOL |
| 2 | 538 | 0.78 | 0.85 | 47 | 3F9 |
| 3 | 250 | 0.56 | 0.77 | 28 | empty |
| 4 | 228 | 0.53 | 0.76 | 24 | empty |
| 5 | 164 | 0.46 | 0.76 | 25 | GOL |
Interfaces
1 interface between chains.
- A–B · 730 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 4TPK · Human butyrylcholinesterase in complex with N-((1-(2,3-dihydro-1H-inden-2-yl)piperidin-3-y… · the same entry in another collection · chain A against A, TM-score 1.00
- P06276 · AlphaFold monomer V2.0 prediction for cholinesterase (P06276) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 4TPK · PDBe 4TPK · UniProt P06276
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