Research workbench
Crystal structure of CK2ALPHA with (methyl 4-((3-(3-chloro-4-(phenyl) BENZYLAMINO)PROPYL)AMINO)-4-oxobutanoate bound
Analyse Crystal structure of CK2ALPHA with (methyl 4-((3-(3-chloro-4-(phenyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CX9
- Type
- protein
- Length
- 653 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
- 551, PO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 328 | 38% helix, 16% strand | P68400 |
| B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 325 | 42% helix, 15% strand | P68400 |
Ligands and binding sites
- 551 · methyl 3-[(3-{[(2-chlorobiphenyl-4-yl)methyl]amino}propyl)amino]-3-oxopropanoate · ligand · 5 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
- ACT · Acetate ion · additive · 6 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.77 | 0.83 | 73 | ACT, 551 |
| 2 | 524 | 0.76 | 0.83 | 62 | ACT, 551 |
| 3 | 499 | 0.62 | 0.76 | 49 | empty |
| 4 | 233 | 0.47 | 0.74 | 28 | empty |
| 5 | 67 | 0.43 | 0.81 | 14 | 551 |
Interfaces
1 interface between chains.
- A–B · 488 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5CX9 · Crystal structure of CK2alpha with (methyl 4-((3-(3-chloro-4-(phenyl)benzylamino)propyl)am… · 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 0.99
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 5CX9 · PDBe 5CX9 · UniProt P68400
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