Research workbench
HDAC8 complexed with a hydroxamic acid
Analyse HDAC8 complexed with a hydroxamic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FCW
- Type
- protein
- Length
- 717 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
- 5YA, ZN, K
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 (EC 3.5.1.98) | protein | 364 | 40% helix, 13% strand | Q9BY41 |
| B | Histone deacetylase 8 (EC 3.5.1.98) | protein | 353 | 40% helix, 13% strand | Q9BY41 |
Ligands and binding sites
- 5YA · 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide · ligand · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- P6G · Hexaethylene glycol · additive · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.83 | 0.85 | 85 | 5YA |
| 2 | 56 | 0.55 | 0.88 | 17 | empty |
| 3 | 113 | 0.46 | 0.79 | 24 | empty |
| 4 | 54 | 0.27 | 0.74 | 12 | empty |
| 5 | 51 | 0.25 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 807 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5FCW · HDAC8 Complexed with a Hydroxamic Acid · 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 5FCW · PDBe 5FCW · UniProt Q9BY41
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