MolNFT v1 · #117649 · protein
Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in complex with belinostat
5EEN · HDAC6 protein: “Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in complex with belinostat”. X-ray diffraction, 4 ligands (5OG, K, ZN), 2 pockets (best druggability 0.42). MolNFT v1 #117649 on GenesisL1: 3D…
- PDB
- 5EEN
- Type
- protein
- Length
- 710 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HDAC6 protein
- EC
- 3.5.1.98
- UniProt
- A7YT55
- Ligands
- 5OG, K, ZN, CL
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | HDAC6 protein (EC 3.5.1.98) | protein | 353 | 44% helix, 14% strand | A7YT55 |
| A | HDAC6 protein (EC 3.5.1.98) | protein | 357 | 43% helix, 14% strand | A7YT55 |
Ligands and binding sites
- 5OG · Belinostat · ligand · 2 copies · chains B, A
- K · Potassium ion · metal · 4 copies · chains B, A
- ZN · Zinc ion · metal · 2 copies · chains B, A
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.42 | 0.74 | 27 | empty |
| 2 | 96 | 0.36 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 274 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5EEN · Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with… · the same entry in another collection · chain B against B, 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 A7YT55
- Elsewhere: RCSB PDB 5EEN · PDBe 5EEN · UniProt A7YT55
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