MolNFT v1 · #115788 · protein
Crystal structure of CK2ALPHA with compound 10 bound
5CU3 · Casein kinase II subunit alpha: “Crystal structure of CK2ALPHA with compound 10 bound”. X-ray diffraction, 2 ligands (54S, PO4), 7 pockets (best druggability 0.77). MolNFT v1 #115788 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5CU3
- Type
- protein
- Length
- 649 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
- 54S, PO4
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 325 | 42% helix, 16% strand | P68400 |
| B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 324 | 41% helix, 16% strand | P68400 |
Ligands and binding sites
- 54S · N-[(2-chlorobiphenyl-4-yl)methyl]-beta-alanyl-N-(3-carboxyphenyl)-beta-alaninamide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
- ACT · Acetate ion · additive · 5 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.77 | 0.83 | 63 | ACT, 54S |
| 2 | 562 | 0.76 | 0.83 | 69 | ACT, 54S |
| 3 | 503 | 0.64 | 0.77 | 45 | empty |
| 4 | 203 | 0.45 | 0.74 | 26 | DMS |
| 5 | 69 | 0.34 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 631 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- P68400 · AlphaFold monomer V2.0 prediction for casein kinase II subunit alpha (P68400) · a predicted model of the same protein · chain A 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 5CU3 · PDBe 5CU3 · UniProt P68400
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