Research workbench
Crystal structure of the human HIPK3 kinase domain bound to abemaciclib
Analyse Crystal structure of the human HIPK3 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
- 7O7J
- Type
- protein
- Length
- 368 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homeodomain-interacting protein kinase 3
- EC
- 2.7.11.1
- UniProt
- Q9H422
- Ligands
- 6ZV
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homeodomain-interacting protein kinase 3 (EC 2.7.11.1) | protein | 368 | 41% helix, 17% strand | Q9H422 |
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 · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.66 | 0.79 | 41 | 6ZV |
| 2 | 95 | 0.39 | 0.76 | 15 | empty |
| 3 | 96 | 0.35 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 7O7J · Crystal structure of the human HIPK3 kinase domain bound to abemaciclib · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H422 · AlphaFold monomer V2.0 prediction for homeodomain-interacting protein kinase 3 (Q9H422) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9H422
- Elsewhere: RCSB PDB 7O7J · PDBe 7O7J · UniProt Q9H422
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