Research workbench
Crystal structure of danio rerio histone deacetylase 10 in complex with 3-thienylmethyl benzhydroxamic acid inhibitor
Analyse Crystal structure of danio rerio histone deacetylase 10 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7U6A
- Type
- protein
- Length
- 639 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyamine deacetylase HDAC10
- EC
- 3.5.1.48, 3.5.1.62
- UniProt
- F1QCV2
- Ligands
- LSL, K, ZN, PO4
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyamine deacetylase HDAC10 (EC 3.5.1.48, 3.5.1.62) | protein | 639 | 41% helix, 15% strand | F1QCV2 |
Ligands and binding sites
- LSL · N-hydroxy-4-({[(thiophen-3-yl)methyl]amino}methyl) benzamide · ligand · chains A
- K · Potassium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.71 | 0.92 | 27 | empty |
| 2 | 215 | 0.67 | 0.85 | 32 | empty |
| 3 | 185 | 0.65 | 0.85 | 36 | empty |
| 4 | 94 | 0.50 | 0.82 | 22 | LSL |
| 5 | 146 | 0.46 | 0.77 | 31 | empty |
Compared structures
- 7U6A · Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with 3-thienylmethyl… · the same entry in another collection · chain A against A, TM-score 1.00
- F1QCV2 · AlphaFold monomer V2.0 prediction for polyamine deacetylase HDAC10 (F1QCV2) · 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 F1QCV2
- Elsewhere: RCSB PDB 7U6A · PDBe 7U6A · UniProt F1QCV2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.