MolNFT v1 · #179121 · protein
Crystal structure of human histone deacetylase 8 (HDAC8) G320R mutation complexed with M344
7JVW: “Crystal structure of human histone deacetylase 8 (HDAC8) G320R mutation complexed with M344”. X-ray diffraction, 3 ligands (B3N, K, ZN), 2 pockets (best druggability 0.82). MolNFT v1 #179121 on GenesisL1: 3D structure, binding sites…
- PDB
- 7JVW
- Type
- protein
- Length
- 706 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, K, ZN
- Pockets
- 2 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 (EC 3.5.1.98) | protein | 354 | 41% helix, 13% strand | Q9BY41 |
| B | Histone deacetylase 8 (EC 3.5.1.98) | protein | 352 | 40% helix, 13% strand | Q9BY41 |
Ligands and binding sites
- B3N · 4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide · 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 | 1150 | 0.82 | 0.83 | 115 | B3N, ZN |
| 2 | 119 | 0.63 | 0.88 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 559 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7JVW · Crystal structure of human histone deacetylase 8 (HDAC8) G320R mutation complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BY41 · AlphaFold monomer V2.0 prediction for histone deacetylase 8 (Q9BY41) · a predicted model of the same protein · 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 7JVW · PDBe 7JVW · UniProt Q9BY41
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