MolNFT v1 · #168302 · protein
Crystal structure of danio rerio histone deacetylase 10 in complex with tubastatin a
6WBQ · Polyamine deacetylase HDAC10: “Crystal structure of danio rerio histone deacetylase 10 in complex with tubastatin a”. X-ray diffraction, 4 ligands (N9W, K, ZN), 8 pockets (best druggability 0.66). MolNFT v1 #168302 on GenesisL1: 3D…
- PDB
- 6WBQ
- Type
- protein
- Length
- 634 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
- N9W, K, ZN, PO4
- Pockets
- 8 · best druggability 0.66
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 | 634 | 41% helix, 15% strand | F1QCV2 |
Ligands and binding sites
- N9W · 4-[(2-methyl-3,4-dihydro-1~{H}-pyrido[4,3-b]indol-5-yl)methyl]-~{N}-oxidanyl-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 · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.66 | 0.84 | 33 | empty |
| 2 | 181 | 0.62 | 0.84 | 37 | EDO |
| 3 | 112 | 0.52 | 0.82 | 29 | N9W |
| 4 | 137 | 0.51 | 0.80 | 26 | empty |
| 5 | 129 | 0.43 | 0.76 | 20 | empty |
Compared structures
- 6WBQ · Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Tubastatin A · 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 6WBQ · PDBe 6WBQ · UniProt F1QCV2
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