Research workbench
Crystal structure of a low occupancy fragment candidate (N-(4-Methyl-1,3-thiazol-2-yl)propanamide) bound adjacent to the ubiquitin binding pocket of the HDAC6 zinc-finger domain
Analyse Crystal structure of a low occupancy fragment candidate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B8D
- Type
- protein
- Length
- 99 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.05
- Source
- Homo sapiens
- Molecule
- Histone deacetylase 6
- EC
- 3.5.1.98
- UniProt
- Q9UBN7
- Ligands
- 6T4, ZN, NA, UNX
- Pockets
- 1 · best druggability 0.40
Structure
x-ray diffraction · resolution 1.05 · 1 distinct chain · 26% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 6 (EC 3.5.1.98) | protein | 99 | 26% helix, 18% strand | Q9UBN7 |
Ligands and binding sites
- 6T4 · ~{N}-(4-methyl-1,3-thiazol-2-yl)ethanamide · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- NA · Sodium ion · metal · chains A
- UNX · Unknown atom or ion · ion · 36 copies · chains A
- FMT · Formic acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.40 | 0.77 | 19 | FMT, 6T4 |
Compared structures
- 5B8D · Crystal structure of a low occupancy fragment candidate (N-(4-methyl… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UBN7 · AlphaFold monomer V2.0 prediction for histone deacetylase 6 (Q9UBN7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9UBN7
- Elsewhere: RCSB PDB 5B8D · PDBe 5B8D · UniProt Q9UBN7
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