Research workbench
Crystal structure of danio rerio histone deacetylase 10 in complex with bishydroxamic acid based inhibitor
Analyse Crystal structure of danio rerio histone deacetylase 10 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VNQ
- 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
- R5G, K, ZN, PO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 40% 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 | 40% helix, 15% strand | F1QCV2 |
Ligands and binding sites
- R5G · N-hydroxy-1-{[4-(hydroxycarbamoyl)phenyl]methyl}-1H-indole-6-carboxamide · 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 · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.69 | 0.89 | 30 | empty |
| 2 | 188 | 0.63 | 0.84 | 34 | empty |
| 3 | 186 | 0.57 | 0.80 | 29 | empty |
| 4 | 112 | 0.52 | 0.82 | 28 | R5G |
| 5 | 91 | 0.43 | 0.79 | 13 | empty |
Compared structures
- 6VNQ · Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Bishydroxamic… · 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 0.99
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 6VNQ · PDBe 6VNQ · UniProt F1QCV2
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