Research workbench
Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in complex with a mercaptoacetamide-based inhibitor
Analyse Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MR5
- Type
- protein
- Length
- 711 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HDAC6 protein
- UniProt
- A7YT55
- Ligands
- W45, K, ZN
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HDAC6 protein | protein | 355 | 43% helix, 13% strand | A7YT55 |
| B | HDAC6 protein | protein | 356 | 44% helix, 14% strand | A7YT55 |
Ligands and binding sites
- W45 · N-[5-(5,6-dichloro-1H-indol-1-yl)pentyl]-2-sulfanylacetamide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- FLC · Citrate anion · additive · chains B
- EDO · 1,2-ethanediol · additive · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.78 | 0.82 | 102 | W45, PEG, ZN |
| 2 | 98 | 0.40 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 407 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6MR5 · Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with… · 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 A7YT55
- Elsewhere: RCSB PDB 6MR5 · PDBe 6MR5 · UniProt A7YT55
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.