Research workbench
Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in complex with ricolinostat (acy-1215)
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
- 5WGL
- Type
- protein
- Length
- 714 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HDAC6 protein
- UniProt
- A7YT55
- Ligands
- AH4, K, ZN
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HDAC6 protein | protein | 358 | 43% helix, 13% strand | A7YT55 |
| B | HDAC6 protein | protein | 356 | 44% helix, 14% strand | A7YT55 |
Ligands and binding sites
- AH4 · 2-(diphenylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]pyrimidine-5-carboxamide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- FLC · Citrate anion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.52 | 0.78 | 34 | EDO |
| 2 | 154 | 0.39 | 0.73 | 26 | EDO |
| 3 | 82 | 0.32 | 0.74 | 15 | empty |
| 4 | 71 | 0.31 | 0.74 | 16 | EDO |
| 5 | 70 | 0.30 | 0.74 | 19 | EDO |
Interfaces
1 interface between chains.
- A–B · 312 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5WGL · 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 5WGL · PDBe 5WGL · UniProt A7YT55
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