Research workbench
Crystal structure of parp catalytic domain in complex with novel inhibitors
Analyse Crystal structure of parp catalytic domain in complex with novel inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HHY
- Type
- protein
- Length
- 1,343 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly [ADP-ribose] polymerase 1
- EC
- 2.4.2.30
- UniProt
- P09874
- Ligands
- 15R, SO4
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 349 | 36% helix, 25% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 340 | 39% helix, 24% strand | P09874 |
| C | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 345 | 38% helix, 22% strand | P09874 |
| D | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 309 | 33% helix, 19% strand | P09874 |
Ligands and binding sites
- 15R · (9aR)-1-[(1-{2-fluoro-5-[(4-oxo-3,4-dihydrophthalazin-1-yl)methyl]benzoyl}piperidin-4-yl)carbonyl]-1,2,3,8,9,9a-hexahydro-7H-benzo[de][1,7]naphthyridin-7-one · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 620 | 0.81 | 0.86 | 50 | 15R |
| 2 | 981 | 0.79 | 0.81 | 88 | 15R, SO4, PEG |
| 3 | 764 | 0.79 | 0.83 | 70 | 15R |
| 4 | 541 | 0.78 | 0.84 | 46 | 15R |
| 5 | 1123 | 0.74 | 0.77 | 105 | empty |
Interfaces
5 interfaces between chains.
- A–B · 936 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 404 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 298 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 230 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 48 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4HHY · 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
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 4HHY · PDBe 4HHY · UniProt P09874
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