MolNFT v1 · #151599 · protein
Crystal structure of a human HDAC8 L6 loop mutant complexed with quisinostat
6HSK · Histone deacetylase 8: “Crystal structure of a human HDAC8 L6 loop mutant complexed with quisinostat”. X-ray diffraction, 3 ligands (GOK, K, ZN), 2 pockets (best druggability 0.74). MolNFT v1 #151599 on GenesisL1: 3D structure…
- PDB
- 6HSK
- Type
- protein
- Length
- 728 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8
- EC
- 3.5.1.98
- UniProt
- Q9BY41
- Ligands
- GOK, K, ZN
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histone deacetylase 8 (EC 3.5.1.98) | protein | 364 | 41% helix, 13% strand | Q9BY41 |
Ligands and binding sites
- GOK · 2-[4-[[(1-methylindol-3-yl) methylamino]methyl]piperidin-1-yl]-~{N}-oxidanyl-pyrimidine-5-carboxamide · 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
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.74 | 0.77 | 84 | GOK |
| 2 | 184 | 0.64 | 0.84 | 43 | ZN, GOK |
Interfaces
1 interface between chains.
- A–B · 278 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6HSK · Crystal structure of a human HDAC8 L6 loop mutant complexed with Quisinostat · 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 Q9BY41
- Elsewhere: RCSB PDB 6HSK · PDBe 6HSK · UniProt Q9BY41
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