MolNFT v1 · #168356 · protein
Crystal structure of danio rerio histone deacetylase 10 in complex with dimethylaminomethylindole phenylhydroxamate inhibitor
6WDV · Polyamine deacetylase HDAC10: “Crystal structure of danio rerio histone deacetylase 10 in complex with dimethylaminomethylindole…”. X-ray diffraction, 4 ligands (TWM, K, ZN), 5 pockets (best druggability 0.64). MolNFT v1 #168356 on…
- PDB
- 6WDV
- Type
- protein
- Length
- 638 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
- TWM, K, ZN, PO4
- Pockets
- 5 · best druggability 0.64
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 | 638 | 41% helix, 15% strand | F1QCV2 |
Ligands and binding sites
- TWM · 4-({3-[(dimethylamino)methyl]-1H-indol-1-yl}methyl)-N-hydroxybenzamide · 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.64 | 0.88 | 18 | empty |
| 2 | 192 | 0.62 | 0.84 | 35 | empty |
| 3 | 122 | 0.59 | 0.84 | 23 | empty |
| 4 | 72 | 0.56 | 0.87 | 19 | TWM |
| 5 | 65 | 0.35 | 0.77 | 20 | empty |
Compared structures
- 6WDV · Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with… · 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 6WDV · PDBe 6WDV · UniProt F1QCV2
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