Research workbench
Tetragonal complex structure of protein kinase CK2 catalytic subunit with a benzotriazole-based inhibitor generated by click-chemistry
Analyse Tetragonal complex structure of protein kinase CK2 catalytic subunit with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CQW
- Type
- protein
- Length
- 662 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
- JRJ, SO4, CL
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 331 | 39% helix, 16% strand | P68400 |
Ligands and binding sites
- JRJ · 4-[4-[2-[4,5,6,7-tetrakis(bromanyl)benzotriazol-2-yl]ethyl]-1,2,3-triazol-1-yl]butan-1-amine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 11 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.72 | 0.83 | 46 | JRJ, SO4 |
| 2 | 412 | 0.72 | 0.82 | 53 | JRJ, SO4 |
| 3 | 109 | 0.46 | 0.79 | 21 | SO4 |
| 4 | 62 | 0.37 | 0.78 | 13 | empty |
| 5 | 51 | 0.29 | 0.76 | 14 | empty |
Compared structures
- 5CQW · Tetragonal Complex Structure of Protein Kinase CK2 Catalytic Subunit with a… · 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 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 5CQW · PDBe 5CQW · UniProt P68400
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.