MolNFT v1 · #78648 · protein
Crystal structure of human HDAC8 inhibitor complex, an amino acid derived inhibitor
3SFF · Histone deacetylase 8: “Crystal structure of human HDAC8 inhibitor complex, an amino acid derived inhibitor”. X-ray diffraction, 3 ligands (0DI, K, ZN), 1 pocket (best druggability 0.72). MolNFT v1 #78648 on GenesisL1: 3D structure…
- PDB
- 3SFF
- Type
- protein
- Length
- 341 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8
- EC
- 3.5.1.98
- UniProt
- Q9BY41
- Ligands
- 0DI, K, ZN
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 (EC 3.5.1.98) | protein | 341 | 43% helix, 14% strand | Q9BY41 |
Ligands and binding sites
- 0DI · (2R)-2-amino-3-(3-chlorophenyl)-1-[4-(2,5-difluorobenzoyl)piperazin-1-yl]propan-1-one · ligand · chains A
- K · Potassium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.72 | 0.89 | 32 | 0DI |
Compared structures
- 3SFF · Crystal Structure of Human HDAC8 Inhibitor Complex, an Amino Acid Derived Inhibitor · 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 3SFF · PDBe 3SFF · UniProt Q9BY41
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