Research workbench
Catalytic domain of human parp-1 in complex with the inhibitor MC2050
Analyse Catalytic domain of human parp-1 in complex with the inhibitor MC2050 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XVW
- Type
- protein
- Length
- 691 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly [ADP-ribose] polymerase 1
- EC
- 2.4.2.30, 2.4.2.-
- UniProt
- P09874
- Ligands
- O3H, NI
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 345 | 39% helix, 25% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 346 | 40% helix, 25% strand | P09874 |
Ligands and binding sites
- O3H · 2-[2-(4-pyridin-2-ylpiperazin-1-yl)ethylsulfanyl]-3~{H}-quinazolin-4-one · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 633 | 0.82 | 0.87 | 64 | O3H |
| 2 | 612 | 0.82 | 0.87 | 56 | NI, O3H |
| 3 | 524 | 0.70 | 0.80 | 51 | NI |
| 4 | 115 | 0.48 | 0.79 | 20 | empty |
| 5 | 148 | 0.48 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1234 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6XVW · Catalytic domain of human PARP-1 in complex with the inhibitor MC2050 · 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 6XVW · PDBe 6XVW · UniProt P09874
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