Research workbench
Structure-based optimization of 1H-imidazole-2-carboxamides as axl kinase inhibitors utilizing a mer mutant surrogate
Analyse Structure-based optimization of 1H-imidazole-2-carboxamides 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
- 5TD2
- Type
- protein
- Length
- 482 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
- 7AE
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 240 | 37% helix, 18% strand | Q12866 |
| B | Tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 242 | 39% helix, 16% strand | Q12866 |
Ligands and binding sites
- 7AE · N-[2-{4-[(2S)-4-(methylsulfonyl)morpholin-2-yl]-1,3-thiazol-2-yl}-4-(morpholin-4-yl)phenyl]-1H-imidazole-2-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.68 | 0.77 | 72 | 7AE |
| 2 | 255 | 0.66 | 0.83 | 34 | empty |
| 3 | 303 | 0.60 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 884 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5TD2 · Structure-based optimization of 1H-imidazole-2-carboxamides as Axl kinase inhibitors… · the same entry in another collection · chain A against A, TM-score 1.00
- Q12866 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase mer (Q12866) · 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 Q12866
- Elsewhere: RCSB PDB 5TD2 · PDBe 5TD2 · UniProt Q12866
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