MolNFT v1 · #150194 · protein
The crystal structure of CK2ALPHA in complex with compound 3
6GMD · Casein kinase II subunit alpha: “The crystal structure of CK2ALPHA in complex with compound 3”. X-ray diffraction, 2 ligands (A8Q, ATP), 13 pockets (best druggability 0.77). MolNFT v1 #150194 on GenesisL1: 3D structure, binding…
- PDB
- 6GMD
- 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
- A8Q, ATP
- Pockets
- 13 · 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 | 325 | 40% helix, 16% strand | P68400 |
| B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 326 | 39% helix, 16% strand | P68400 |
Ligands and binding sites
- A8Q · [3-chloranyl-4-(2-propan-2-ylphenyl) phenyl]methylazanium · ligand · 3 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, 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
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.77 | 0.83 | 69 | ACT, A8Q, ATP |
| 2 | 197 | 0.73 | 0.89 | 31 | A8Q |
| 3 | 481 | 0.69 | 0.79 | 47 | ACT, ATP |
| 4 | 488 | 0.64 | 0.77 | 37 | empty |
| 5 | 120 | 0.47 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 548 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6GMD · The crystal structure of CK2alpha in complex with compound 3 · 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 6GMD · PDBe 6GMD · UniProt P68400
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