MolNFT v2 · #227375 · protein
Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with m-Aminomethyl Phenylthioketone
9CBF · Polyamine deacetylase HDAC10: “Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with m-Aminomethyl Phenylthioketone”. X-ray diffraction at 2.26, 4 ligands (A1AVR, K, ZN), 6 pockets (best druggability 0.61). MolNFT…
- PDB
- 9CBF
- Type
- protein
- Length
- 609 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.26
- Source
- Danio rerio
- Molecule
- Polyamine deacetylase HDAC10
- EC
- 3.5.1.48, 3.5.1.62
- UniProt
- F1QCV2
- Ligands
- A1AVR, K, ZN, PO4
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · resolution 2.26 · 1 distinct chain · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyamine deacetylase HDAC10 (EC 3.5.1.48, 3.5.1.62) | protein | 609 | 42% helix, 14% strand | F1QCV2 |
Ligands and binding sites
- A1AVR · 1-[3-(aminomethyl)phenyl]-2-sulfanylethan-1-one · ligand · chains A
- K · Potassium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.61 | 0.85 | 32 | empty |
| 2 | 192 | 0.59 | 0.81 | 28 | empty |
| 3 | 54 | 0.52 | 0.88 | 18 | A1AVR |
| 4 | 138 | 0.49 | 0.78 | 27 | empty |
| 5 | 56 | 0.39 | 0.80 | 19 | empty |
Compared structures
- F1QCV2 · AlphaFold monomer V2.0 prediction for polyamine deacetylase HDAC10 (F1QCV2) · a predicted model of the same protein · chain A 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 F1QCV2
- Elsewhere: RCSB PDB 9CBF · PDBe 9CBF · UniProt F1QCV2
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