Research workbench
Crystal structure of the human DYRK1A kinase domain bound to abemaciclib
Analyse Crystal structure of the human DYRK1A kinase domain bound to abemaciclib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O7K
- Type
- protein
- Length
- 690 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual specificity tyrosine-phosphorylation-regulated kinase 1A
- EC
- 2.7.12.1
- UniProt
- Q13627
- Ligands
- 6ZV, LI
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 345 | 35% helix, 19% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 345 | 36% helix, 19% strand | Q13627 |
Ligands and binding sites
- 6ZV · N-{5-[(4-ethylpiperazin-1-yl)methyl]pyridin-2-yl}-5-fluoro-4-[4-fluoro-2-methyl-1-(propan-2-yl)-1H-benzimidazol-6-yl]pyrimidin-2-amine · ligand · 2 copies · chains A, B
- LI · Lithium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 20 copies · chains A, B
- FLC · Citrate anion · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 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 | 1028 | 0.79 | 0.80 | 100 | EDO, FLC, 6ZV, LI |
| 2 | 782 | 0.76 | 0.80 | 78 | FLC, 6ZV, EDO, LI |
| 3 | 77 | 0.42 | 0.79 | 18 | empty |
| 4 | 78 | 0.40 | 0.78 | 18 | empty |
| 5 | 92 | 0.35 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1306 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 7O7K · Crystal structure of the human DYRK1A kinase domain bound to abemaciclib · the same entry in another collection · chain A against A, TM-score 1.00
- Q13627 · AlphaFold monomer V2.0 prediction for dual specificity tyrosine… · a predicted model of the same protein · chain B 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 Q13627
- Elsewhere: RCSB PDB 7O7K · PDBe 7O7K · UniProt Q13627
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