Research workbench
Novel orally efficacious inhibitors complexed with PARP1
Analyse Novel orally efficacious inhibitors complexed with PARP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XSU
- Type
- protein
- Length
- 1,338 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
- 8E3, SO4
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 346 | 39% helix, 24% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 340 | 37% helix, 25% strand | P09874 |
| C | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 328 | 38% helix, 24% strand | P09874 |
| D | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 324 | 35% helix, 23% strand | P09874 |
Ligands and binding sites
- 8E3 · 6-fluoranyl-2-(4,5,6,7-tetrahydrofuro[2,3-c]pyridin-2-yl)-1~{H}-benzimidazole-4-carboxamide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.76 | 0.79 | 91 | SO4, 8E3 |
| 2 | 546 | 0.75 | 0.83 | 60 | SO4, 8E3 |
| 3 | 845 | 0.75 | 0.79 | 68 | SO4, 8E3 |
| 4 | 532 | 0.73 | 0.81 | 46 | SO4, 8E3 |
| 5 | 917 | 0.72 | 0.76 | 80 | empty |
Interfaces
4 interfaces between chains.
- A–B · 816 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 291 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 141 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 117 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5XSU · novel orally efficacious inhibitors complexed with PARP1 · the same entry in another collection · chain D against D, 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 5XSU · PDBe 5XSU · UniProt P09874
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