Linked KDM5A jmj domain forming covalent bond to inhibitor N71 I.E. 2- ((3-(4-(DIMETHYLAMINO)BUT-2-ENAMIDO)PHENYL)(2-(piperidin-1-yl) ETHOXY)METHYL)THIENO[3,2-B]PYRIDINE-7-carboxylic acid

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 24% strand (DSSP).

Ligands and binding sites

• H77 · 2-{(R)-(3-{[(2E)-4-(dimethylamino)but-2-enoyl]amino}phenyl)[2-(piperidin-1-yl) ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid · ligand · chains A
• HZV · 2-{(R)-(3-{[4-(dimethylamino)butanoyl]amino}phenyl)[2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid · ligand · chains A
• HZM · 2-{(S)-(3-{[4-(dimethylamino)butanoyl]amino}phenyl)[2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid · ligand · chains A
• MN · Manganese (II) ion · metal · chains A
• GOL · Glycerol · additive · 2 copies · chains A
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 6DQB · LINKED KDM5A JMJ DOMAIN FORMING COVALENT BOND TO INHIBITOR N71 i.e.… · the same entry in another collection · chain A against A, TM-score 1.00
• P29375 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 5A (P29375) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P29375
• Elsewhere: RCSB PDB 6DQB · PDBe 6DQB · UniProt P29375