Research workbench
Structure of the axl kinase domain in complex with a macrocyclic inhibitor
Analyse Structure of the axl kinase domain in complex with a macrocyclic inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U6B
- Type
- protein
- Length
- 1,122 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase receptor ufo
- EC
- 2.7.10.1
- UniProt
- P30530
- Ligands
- 7YS
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tyrosine-protein kinase receptor ufo (EC 2.7.10.1) | protein | 270 | 44% helix, 17% strand | P30530 |
| B, D | Tyrosine-protein kinase receptor ufo (EC 2.7.10.1) | protein | 291 | 39% helix, 16% strand | P30530 |
Ligands and binding sites
- 7YS · (10R)-7-amino-11-chloro-12-fluoro-1-(2-hydroxyethyl)-3, 10,16-trimethyl-16,17-dihydro-1H-8,4-(azeno) pyrazolo[4,3-h][2,5,11]benzoxadiazacyclotetradecin-15(10H)-one · ligand · 4 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.77 | 0.80 | 68 | 7YS |
| 2 | 1094 | 0.75 | 0.77 | 90 | 7YS |
| 3 | 421 | 0.65 | 0.79 | 45 | empty |
| 4 | 299 | 0.65 | 0.81 | 35 | 7YS |
| 5 | 364 | 0.64 | 0.79 | 35 | 7YS |
Interfaces
5 interfaces between chains.
- B–C · 782 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 601 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 579 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 77 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 57 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5U6B · Structure of the Axl kinase domain in complex with a macrocyclic inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P30530 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase receptor ufo (P30530) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P30530
- Elsewhere: RCSB PDB 5U6B · PDBe 5U6B · UniProt P30530
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