Research workbench
Structure of PARP1 catalytic domain bound to inhibitor bmn 673
Analyse Structure of PARP1 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
- 4PJT
- Type
- protein
- Length
- 1,342 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
- 2YQ, SO4
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 338 | 39% helix, 25% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 332 | 40% helix, 25% strand | P09874 |
| C | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 346 | 39% helix, 25% strand | P09874 |
| D | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 326 | 39% helix, 25% strand | P09874 |
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 · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 15 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.78 | 0.85 | 44 | SO4, 2YQ |
| 2 | 532 | 0.78 | 0.85 | 43 | 2YQ, GOL |
| 3 | 495 | 0.77 | 0.84 | 45 | SO4, 2YQ |
| 4 | 558 | 0.77 | 0.83 | 45 | 2YQ |
| 5 | 875 | 0.73 | 0.77 | 81 | SO4 |
Interfaces
5 interfaces between chains.
- A–C · 647 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 441 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 348 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 346 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 186 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4PJT · Structure of PARP1 catalytic domain bound to inhibitor BMN 673 · 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 4PJT · PDBe 4PJT · UniProt P09874
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