Research workbench
Crystal structure of HDAC8 in complex with compound 30
Analyse Crystal structure of HDAC8 in complex with compound 30 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ODC
- Type
- protein
- Length
- 1,087 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
- M7Y, K, ZN
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 (EC 3.5.1.98) | protein | 367 | 43% helix, 13% strand | Q9BY41 |
| B | Histone deacetylase 8 (EC 3.5.1.98) | protein | 366 | 42% helix, 13% strand | Q9BY41 |
| C | Histone deacetylase 8 (EC 3.5.1.98) | protein | 354 | 42% helix, 13% strand | Q9BY41 |
Ligands and binding sites
- M7Y · (2E)-3-[2-(3-cyclopentyl-5,5-dimethyl-2-oxoimidazolidin-1-yl)phenyl]-N-hydroxyprop-2-enamide · 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
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.76 | 0.81 | 80 | EDO |
| 2 | 52 | 0.71 | 0.98 | 17 | empty |
| 3 | 220 | 0.70 | 0.86 | 43 | M7Y |
| 4 | 326 | 0.63 | 0.79 | 39 | ZN, M7Y |
| 5 | 195 | 0.53 | 0.78 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 712 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 428 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ODC · Crystal structure of HDAC8 in complex with compound 30 · 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 6ODC · PDBe 6ODC · UniProt Q9BY41
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