Research workbench
Fragment-based lead discovery of indazole-based compounds as axl kinase inhibitors
Analyse Fragment-based lead discovery of indazole-based compounds as axl kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DXL
- Type
- protein
- Length
- 517 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase mer
- EC
- 2.7.10.1
- UniProt
- Q12866
- Ligands
- E56
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 261 | 43% helix, 17% strand | Q12866 |
| B | Tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 256 | 40% helix, 16% strand | Q12866 |
Ligands and binding sites
- E56 · 3-[4-[6-chloranyl-5-[[(3R)-pyrrolidin-3-yl]amino]-1H-indazol-3-yl]pyrazol-1-yl]benzenecarbonitrile · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.69 | 0.81 | 41 | E56 |
| 2 | 278 | 0.65 | 0.81 | 35 | E56 |
| 3 | 151 | 0.60 | 0.84 | 18 | empty |
| 4 | 209 | 0.51 | 0.77 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 1055 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7DXL · Fragment-based Lead Discovery of Indazole-based Compounds as AXL Kinase Inhibitors · 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 Q12866
- Elsewhere: RCSB PDB 7DXL · PDBe 7DXL · UniProt Q12866
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