Research workbench
Structure of PARP2 catalytic domain bound to inhibitor bmn 673
Analyse Structure of PARP2 catalytic domain bound to inhibitor bmn 673 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PJV
- Type
- protein
- Length
- 669 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly [ADP-ribose] polymerase 2
- EC
- 2.4.2.30
- UniProt
- Q9UGN5
- Ligands
- 2YQ
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30) | protein | 339 | 37% helix, 24% strand | Q9UGN5 |
| B | Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30) | protein | 330 | 37% helix, 25% strand | Q9UGN5 |
Ligands and binding sites
- 2YQ · (8S,9R)-5-fluoro-8-(4-fluorophenyl)-9-(1-methyl-1H-1,2, 4-triazol-5-yl)-2,7,8,9-tetrahydro-3H-pyrido[4,3,2-de]phthalazin-3-one · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.78 | 0.83 | 56 | 2YQ, GOL |
| 2 | 493 | 0.76 | 0.84 | 46 | 2YQ |
| 3 | 134 | 0.48 | 0.78 | 21 | empty |
| 4 | 115 | 0.46 | 0.79 | 21 | empty |
| 5 | 167 | 0.43 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 234 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4PJV · Structure of PARP2 catalytic domain bound to inhibitor BMN 673 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UGN5 · AlphaFold monomer V2.0 prediction for poly [ADP-ribose] polymerase 2 (Q9UGN5) · a predicted model of the same protein · chain B 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 Q9UGN5
- Elsewhere: RCSB PDB 4PJV · PDBe 4PJV · UniProt Q9UGN5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.