Research workbench
Complex structure of PARP1 catalytic domain with pamiparib
Analyse Complex structure of PARP1 catalytic domain with pamiparib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CMW
- Type
- protein
- Length
- 700 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
- DS9
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 350 | 39% helix, 25% strand | P09874 |
Ligands and binding sites
- DS9 · (2R)-14-fluoro-2-methyl-6,9,10,19-tetrazapentacyclo[14.2.1.02,6.08,18.012,17]nonadeca-1(18),8,12(17),13,15-pentaen-11-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
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 809 | 0.83 | 0.86 | 73 | DS9, GOL |
| 2 | 427 | 0.80 | 0.88 | 46 | DS9, GOL |
| 3 | 180 | 0.52 | 0.78 | 28 | empty |
| 4 | 84 | 0.51 | 0.84 | 15 | empty |
| 5 | 77 | 0.49 | 0.84 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 964 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7CMW · Complex structure of PARP1 catalytic domain with pamiparib · 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 7CMW · PDBe 7CMW · UniProt P09874
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