MolNFT v1 · #87808 · protein
Fragment-based discovery of 6 azaindazoles as inhibitors of bacterial DNA ligase
4CC6: “Fragment-based discovery of 6 azaindazoles as inhibitors of bacterial DNA ligase”. X-ray diffraction, 2 ligands (L5Y, SO4), 5 pockets (best druggability 0.66). MolNFT v1 #87808 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4CC6
- 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
- L5Y, SO4
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase (EC 6.5.1.2) | protein | 308 | 39% helix, 22% strand | Q9AIU7 |
Ligands and binding sites
- L5Y · 2-{[2-(1H-pyrazolo[3,4-c]pyridin-3-yl)-6-(trifluoromethyl)pyridin-4-yl]amino}ethanol · 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.66 | 0.81 | 44 | SO4, L5Y |
| 2 | 146 | 0.53 | 0.80 | 24 | empty |
| 3 | 201 | 0.49 | 0.76 | 29 | empty |
| 4 | 54 | 0.38 | 0.80 | 13 | empty |
| 5 | 93 | 0.36 | 0.75 | 18 | empty |
Compared structures
- 4CC6 · 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 4CC6 · PDBe 4CC6 · UniProt Q9AIU7
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