MolNFT v1 · #166981 · protein
Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 (CD2) complexed with NF2376
6V79 · HDAC6 protein: “Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 (CD2) complexed with NF2376”. X-ray diffraction, 3 ligands (QQD, K, ZN), 3 pockets (best druggability 0.61). MolNFT v1 #166981 on GenesisL1…
- PDB
- 6V79
- 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
- QQD, K, ZN
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | HDAC6 protein | protein | 357 | 43% helix, 14% strand | A7YT55 |
Ligands and binding sites
- QQD · 4-{[(2S)-3,3-dimethyl-2-(pyridin-3-yl)-2,3-dihydro-1H-indol-1-yl]methyl}-N-hydroxybenzamide · 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 · chains A
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 | 347 | 0.61 | 0.78 | 43 | QQD |
| 2 | 124 | 0.49 | 0.79 | 19 | empty |
| 3 | 188 | 0.48 | 0.76 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 407 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6V79 · Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) complexed… · 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 6V79 · PDBe 6V79 · UniProt A7YT55
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