MolNFT v1 · #178881 · protein
Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 complexed with to-317
7JOM · HDAC6 protein: “Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 complexed with to-317”. X-ray diffraction, 3 ligands (TO3, K, ZN), 3 pockets (best druggability 0.57). MolNFT v1 #178881 on GenesisL1: 3D…
- PDB
- 7JOM
- Type
- protein
- Length
- 709 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HDAC6 protein
- EC
- 3.-.-.-
- UniProt
- A7YT55
- Ligands
- TO3, K, ZN
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HDAC6 protein (EC 3.-.-.-) | protein | 355 | 44% helix, 14% strand | A7YT55 |
| B | HDAC6 protein (EC 3.-.-.-) | protein | 354 | 43% helix, 14% strand | A7YT55 |
Ligands and binding sites
- TO3 · N-hydroxy-4-({[(pyridin-3-yl)methyl][(2,3,4,5-tetrafluorophenyl)sulfonyl]amino}methyl)benzamide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 5 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.57 | 0.74 | 50 | empty |
| 2 | 144 | 0.47 | 0.78 | 33 | empty |
| 3 | 65 | 0.39 | 0.79 | 17 | TO3, ZN |
Interfaces
1 interface between chains.
- A–B · 342 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7JOM · Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed 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 7JOM · PDBe 7JOM · UniProt A7YT55
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