MolNFT v1 · #115775 · protein
Crystal structure of CK2ALPHA with N-(3-(3-chloro-4-(phenyl) BENZYLAMINO)PROPYL)ACETAMIDE bound
5CTP · Casein kinase II subunit alpha: “Crystal structure of CK2ALPHA with N-(3-(3-chloro-4-(phenyl) BENZYLAMINO)PROPYL)ACETAMIDE bound”. X-ray diffraction, 2 ligands (54R, PO4), 9 pockets (best druggability 0.78). MolNFT v1 #115775 on…
- PDB
- 5CTP
- Type
- protein
- Length
- 651 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, PO4
- Pockets
- 9 · best druggability 0.78
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 | 324 | 40% helix, 16% strand | P68400 |
| B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 327 | 38% helix, 16% strand | P68400 |
Ligands and binding sites
- 54R · N-(3-{[(2-chlorobiphenyl-4-yl)methyl]amino}propyl)acetamide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
- ACT · Acetate ion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 584 | 0.78 | 0.84 | 57 | ACT, 54R |
| 2 | 582 | 0.75 | 0.81 | 61 | ACT, 54R |
| 3 | 431 | 0.61 | 0.76 | 35 | empty |
| 4 | 353 | 0.55 | 0.74 | 43 | empty |
| 5 | 75 | 0.39 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 523 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5CTP · Crystal structure of CK2alpha with N-(3-(3-chloro-4-(phenyl)benzylamino)propyl)acetamide… · 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 5CTP · PDBe 5CTP · UniProt P68400
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