Research workbench
Crystal structure of CK2ALPHA with 2-hydroxy-5-methylbenzoic acid and N-(3-(3-chloro-4-(PHENYL)BENZYLAMINO)PROPYL)ACETAMIDE bound
Analyse Crystal structure of CK2ALPHA with 2-hydroxy-5-methylbenzoic acid and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CU0
- Type
- protein
- Length
- 652 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
- 54R, 54G
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 327 | 40% helix, 16% strand | P68400 |
| B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 325 | 39% helix, 16% strand | P68400 |
Ligands and binding sites
- 54R · N-(3-{[(2-chlorobiphenyl-4-yl)methyl]amino}propyl)acetamide · ligand · 4 copies · chains A, B
- 54G · 2-hydroxy-5-methylbenzoic acid · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.77 | 0.83 | 70 | 54R, 54G, ACT |
| 2 | 581 | 0.77 | 0.83 | 67 | 54R, 54G |
| 3 | 544 | 0.65 | 0.76 | 48 | empty |
| 4 | 59 | 0.41 | 0.82 | 20 | empty |
| 5 | 87 | 0.41 | 0.78 | 14 | 54R |
Interfaces
1 interface between chains.
- A–B · 516 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5CU0 · Crystal structure of CK2alpha with 2-hydroxy-5-methylbenzoic acid and… · 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 5CU0 · PDBe 5CU0 · UniProt P68400
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