Research workbench
The crystal structure of CK2ALPHA in complex with compound 30
Analyse The crystal structure of CK2ALPHA in complex with compound 30 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OTO
- Type
- protein
- Length
- 651 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Casein kinase II subunit alpha
- EC
- 2.7.11.1
- UniProt
- P68400
- Ligands
- AQW, PO4
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 324 | 39% helix, 16% strand | P68400 |
| A | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 327 | 38% helix, 16% strand | P68400 |
Ligands and binding sites
- AQW · 2-(5-chloranyl-1~{H}-benzimidazol-2-yl)-~{N}-[[3-chloranyl-4-(2-ethylphenyl)phenyl]methyl]ethanamine · ligand · 2 copies · chains B, A
- PO4 · Phosphate ion · ion · 2 copies · chains B, A
- ACT · Acetate ion · additive · 7 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.79 | 0.83 | 68 | ACT, AQW |
| 2 | 697 | 0.76 | 0.81 | 79 | ACT, AQW |
| 3 | 404 | 0.60 | 0.76 | 38 | empty |
| 4 | 230 | 0.48 | 0.74 | 28 | empty |
| 5 | 67 | 0.38 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- B–A · 506 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5OTO · The crystal structure of CK2alpha in complex with compound 30 · the same entry in another collection · chain B against B, TM-score 1.00
- P68400 · AlphaFold monomer V2.0 prediction for casein kinase II subunit alpha (P68400) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P68400
- Elsewhere: RCSB PDB 5OTO · PDBe 5OTO · UniProt P68400
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