Research workbench
Fragment-based discovery of 6 azaindazoles as inhibitors of bacterial DNA ligase
Analyse Fragment-based discovery of 6 azaindazoles as inhibitors of bacterial DNA ligase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CC5
- Type
- protein
- Length
- 308 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase
- EC
- 6.5.1.2
- UniProt
- Q9AIU7
- Ligands
- L5V, SO4
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase (EC 6.5.1.2) | protein | 308 | 41% helix, 22% strand | Q9AIU7 |
Ligands and binding sites
- L5V · 2-chloranyl-6-(1H-1,2,4-triazol-3-yl)pyrazine · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.66 | 0.82 | 42 | SO4, L5V |
| 2 | 314 | 0.58 | 0.77 | 46 | empty |
| 3 | 142 | 0.52 | 0.80 | 24 | empty |
| 4 | 83 | 0.33 | 0.74 | 16 | empty |
Compared structures
- 4CC5 · Fragment-Based Discovery of 6 Azaindazoles As Inhibitors of Bacterial DNA Ligase · the same entry in another collection · chain A against A, TM-score 1.00
- Q9AIU7 · AlphaFold monomer V2.0 prediction for DNA ligase (Q9AIU7) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9AIU7
- Elsewhere: RCSB PDB 4CC5 · PDBe 4CC5 · UniProt Q9AIU7
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