MolNFT v1 · #104425 · protein
Crystal structure of C153F HDAC8 in complex with saha
4QA0 · Histone deacetylase 8: “Crystal structure of C153F HDAC8 in complex with saha”. X-ray diffraction, 3 ligands (SHH, K, ZN), 1 pocket (best druggability 0.81). MolNFT v1 #104425 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4QA0
- Type
- protein
- Length
- 735 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
- SHH, K, ZN
- Pockets
- 1 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 (EC 3.5.1.98) | protein | 371 | 39% helix, 13% strand | Q9BY41 |
| B | Histone deacetylase 8 (EC 3.5.1.98) | protein | 364 | 39% helix, 13% strand | Q9BY41 |
Ligands and binding sites
- SHH · Octanedioic acid hydroxyamide phenylamide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
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 | 933 | 0.81 | 0.83 | 102 | SHH, ZN, GOL |
Interfaces
1 interface between chains.
- A–B · 863 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 4QA0 · PDBe 4QA0 · UniProt Q9BY41
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