MolNFT v1 · #146878 · protein
Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in complex with ddk-115
6DVL · HDAC6 protein: “Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in complex with ddk-115”. X-ray diffraction, 3 ligands (HBG, K, ZN), 3 pockets (best druggability 0.43). MolNFT v1 #146878 on GenesisL1: 3D…
- PDB
- 6DVL
- Type
- protein
- Length
- 711 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HDAC6 protein
- UniProt
- A7YT55
- Ligands
- HBG, K, ZN
- Pockets
- 3 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HDAC6 protein | protein | 356 | 43% helix, 14% strand | A7YT55 |
| B | HDAC6 protein | protein | 355 | 42% helix, 14% strand | A7YT55 |
Ligands and binding sites
- HBG · N-[2-(cyclohexylamino)-2-oxoethyl]-N-{[4-(hydroxycarbamoyl)phenyl]methyl}-3,5-dimethylbenzamide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.43 | 0.73 | 26 | empty |
| 2 | 114 | 0.36 | 0.73 | 30 | empty |
| 3 | 50 | 0.24 | 0.73 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 346 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6DVL · Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with… · the same entry in another collection · 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 A7YT55
- Elsewhere: RCSB PDB 6DVL · PDBe 6DVL · UniProt A7YT55
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