X-ray structure of the danio rerio histone deacetylase 6 (HDAC6; catalytic domain 2) in complex with tubastatin a

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 14% strand (DSSP).

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 · 3 copies · chains A
• ZN · Zinc ion · metal · chains A
• NA · Sodium ion · metal · chains A
• SCN · Thiocyanate ion · ion · 2 copies · chains A
• EDO · 1,2-ethanediol · additive · 2 copies · chains A
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
• GOL · Glycerol · additive · 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.

Compared structures

• 6THV · X-ray structure of the Danio rerio histone deacetylase 6 (HDAC6; catalytic domain 2) in… · 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 F8W4B7
• Elsewhere: RCSB PDB 6THV · PDBe 6THV · UniProt F8W4B7