MolNFT v1 · #147588 · protein
The crystal structure of CK2ALPHA in complex with compound 32
6EHU · Casein kinase II subunit alpha: “The crystal structure of CK2ALPHA in complex with compound 32”. X-ray diffraction, 1 ligand (B5E), 10 pockets (best druggability 0.75). MolNFT v1 #147588 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6EHU
- Type
- protein
- Length
- 654 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
- B5E
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 327 | 40% helix, 15% strand | P68400 |
Ligands and binding sites
- B5E · 2-(1~{H}-benzimidazol-2-yl)-~{N}-[[4-(2-ethylphenyl)-3-(trifluoromethyl)phenyl]methyl]ethanamine · ligand · 6 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.75 | 0.84 | 56 | B5E, ACT |
| 2 | 401 | 0.74 | 0.84 | 52 | B5E, ACT |
| 3 | 537 | 0.69 | 0.78 | 51 | B5E |
| 4 | 50 | 0.56 | 0.91 | 20 | empty |
| 5 | 184 | 0.54 | 0.79 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 308 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6EHU · The crystal structure of CK2alpha in complex with compound 32 · the same entry in another collection · chain A against A, 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 0.98
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 P68400
- Elsewhere: RCSB PDB 6EHU · PDBe 6EHU · UniProt P68400
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