Crystal structure of parp catalytic domain in complex with novel inhibitors

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 24% strand (DSSP).

Ligands and binding sites

• 15S · N-{(2S)-1-[4-(4-fluorophenyl)-3,6-dihydropyridin-1(2H)-yl]-1-oxopropan-2-yl}-2-[(9aR)-7-oxo-2,3,7,8,9,9a-hexahydro-1H-benzo[de][1,7]naphthyridin-1-yl]acetamide · ligand · 4 copies · chains A, B, C, D
• SO4 · Sulfate ion · ion · 3 copies · chains A, B, D

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

Pockets

11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–B · 920 Ų buried · 4 hydrogen bonds · protein-protein
• B–D · 444 Ų buried · 3 hydrogen bonds · protein-protein
• A–C · 423 Ų buried · 7 hydrogen bonds · protein-protein
• B–C · 288 Ų buried · 1 hydrogen bond · protein-protein
• A–D · 178 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 4HHZ · Crystal structure of PARP catalytic domain in complex with novel inhibitors · the same entry in another collection · chain A against A, TM-score 1.00
• P09874 · AlphaFold monomer V2.0 prediction for poly [ADP-ribose] polymerase 1 (P09874) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 P09874
• Elsewhere: RCSB PDB 4HHZ · PDBe 4HHZ · UniProt P09874