Research workbench
Crystal structure of HDAC8 in complex with compound 2
Analyse Crystal structure of HDAC8 in complex with compound 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ODA
- Type
- protein
- Length
- 1,080 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8
- EC
- 3.5.1.98
- UniProt
- Q9BY41
- Ligands
- C7, K, ZN
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 (EC 3.5.1.98) | protein | 364 | 41% helix, 13% strand | Q9BY41 |
| B | Histone deacetylase 8 (EC 3.5.1.98) | protein | 363 | 42% helix, 13% strand | Q9BY41 |
| C | Histone deacetylase 8 (EC 3.5.1.98) | protein | 353 | 41% helix, 13% strand | Q9BY41 |
Ligands and binding sites
- C7 · N-{2-[3-(hydroxyamino)-3-oxopropyl]phenyl}-3-(trifluoromethyl)benzamide · ligand · 3 copies · chains A, B, C
- K · Potassium ion · metal · 6 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 806 | 0.77 | 0.81 | 75 | C7, ZN |
| 2 | 54 | 0.72 | 0.99 | 21 | empty |
| 3 | 355 | 0.57 | 0.75 | 45 | empty |
| 4 | 108 | 0.48 | 0.80 | 21 | C7, ZN |
| 5 | 139 | 0.45 | 0.77 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 664 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 428 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 32 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ODA · Crystal structure of HDAC8 in complex with compound 2 · 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 6ODA · PDBe 6ODA · UniProt Q9BY41
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