MolNFT v1 · #168359 · protein
Crystal structure of danio rerio histone deacetylase 10 in complex with indole phenylhydroxamate inhibitor
6WDY · Polyamine deacetylase HDAC10: “Crystal structure of danio rerio histone deacetylase 10 in complex with indole phenylhydroxamate inhibitor”. X-ray diffraction, 4 ligands (TWP, K, ZN), 9 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 6WDY
- Type
- protein
- Length
- 635 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyamine deacetylase HDAC10
- EC
- 3.5.1.48, 3.5.1.62
- UniProt
- F1QCV2
- Ligands
- TWP, K, ZN, PO4
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyamine deacetylase HDAC10 (EC 3.5.1.48, 3.5.1.62) | protein | 635 | 41% helix, 15% strand | F1QCV2 |
Ligands and binding sites
- TWP · N-hydroxy-4-[(1H-indol-1-yl)methyl]benzamide · ligand · chains A
- K · Potassium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.74 | 0.89 | 42 | empty |
| 2 | 208 | 0.66 | 0.84 | 36 | empty |
| 3 | 226 | 0.65 | 0.83 | 30 | empty |
| 4 | 99 | 0.53 | 0.83 | 29 | TWP, EDO |
| 5 | 53 | 0.36 | 0.79 | 16 | empty |
Compared structures
- 6WDY · Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Indole… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 6WDY · PDBe 6WDY · UniProt F1QCV2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.