MolNFT v1 · #134870 · protein
Crystal structure of G304A HDAC8 in complex with M344
5THU · Histone deacetylase 8: “Crystal structure of G304A HDAC8 in complex with M344”. X-ray diffraction, 4 ligands (B3N, GGG, K), 4 pockets (best druggability 0.73). MolNFT v1 #134870 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5THU
- Type
- protein
- Length
- 702 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
- B3N, GGG, K, ZN
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 (EC 3.5.1.98) | protein | 358 | 40% helix, 14% strand | Q9BY41 |
| B | Histone deacetylase 8 (EC 3.5.1.98) | protein | 344 | 42% helix, 14% strand | Q9BY41 |
Ligands and binding sites
- B3N · 4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide · ligand · 2 copies · chains A, B
- GGG · glycylglycylglycine · ligand · 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.73 | 0.77 | 111 | B3N |
| 2 | 67 | 0.64 | 0.93 | 19 | empty |
| 3 | 60 | 0.35 | 0.78 | 16 | empty |
| 4 | 58 | 0.30 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 632 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5THU · Crystal Structure of G304A HDAC8 in complex with M344 · 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 5THU · PDBe 5THU · UniProt Q9BY41
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