Research workbench
Crystal structure of tcache complexed to 1-(6-oxo-1,2,3,4,6,10B- HEXAHYDROPYRIDO[2,1-A]ISOINDOL-10-yl)-3-(4-(((1-(2-((1,2,3,4- tetrahydroacridin-9-YL)AMINO)ETHYL)-1H-1,2,3-triazol-4-YL)METHOXY) METHYL)PYRIDIN-2-YL)UREA
Analyse Crystal structure of tcache complexed to 1-(6-oxo-1,2,3,4,6,10B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H12
- Type
- protein
- Length
- 1,064 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholinesterase
- EC
- 3.1.1.7
- UniProt
- P04058
- Ligands
- FJK, NAG, CL, SO4
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acetylcholinesterase (EC 3.1.1.7) | protein | 532 | 40% helix, 17% strand | P04058 |
Ligands and binding sites
- FJK · 1-[4-[[1-[2-(1,2,3,4,4~{A},9~{A}-hexahydroacridin-9-ylamino)ethyl]-1,2,3-triazol-4-yl]methoxymethyl]pyridin-2-yl]-3-[(10~{B}~{R})-6-oxidanylidene-2,3,4,10~{B}-tetrahydro-1~{H}-pyrido[2, 1-a]isoindol-10-yl]urea · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 8 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.76 | 0.86 | 42 | FJK |
| 2 | 346 | 0.75 | 0.86 | 40 | FJK |
| 3 | 602 | 0.64 | 0.75 | 50 | GOL, EDO, PEG, CL |
| 4 | 359 | 0.59 | 0.76 | 33 | EDO |
| 5 | 349 | 0.58 | 0.76 | 33 | PGE, GOL, EDO, PEG |
Interfaces
1 interface between chains.
- A–B · 265 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6H12 · Crystal structure of TcACHE complexed to 1-(6-Oxo-1,2,3,4,6,10b-hexahydropyrido[2,1-a]isoi… · the same entry in another collection · chain A against A, TM-score 1.00
- P04058 · AlphaFold monomer V2.0 prediction for acetylcholinesterase (P04058) · 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 P04058
- Elsewhere: RCSB PDB 6H12 · PDBe 6H12 · UniProt P04058
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