MolNFT v1 · #129677 · protein
The crystal structure of CK2ALPHA in complex with compound 2
5ORH · Casein kinase II subunit alpha: “The crystal structure of CK2ALPHA in complex with compound 2”. X-ray diffraction, 1 ligand (A4N), 13 pockets (best druggability 0.76). MolNFT v1 #129677 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5ORH
- Type
- protein
- Length
- 649 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
- A4N
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 324 | 41% helix, 16% strand | P68400 |
| B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 325 | 41% helix, 15% strand | P68400 |
Ligands and binding sites
- A4N · [3-chloranyl-4-(2-methylphenyl)phenyl]methanamine · ligand · 4 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains 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 | 468 | 0.76 | 0.84 | 58 | A4N, ACT |
| 2 | 134 | 0.75 | 0.93 | 23 | A4N |
| 3 | 343 | 0.68 | 0.81 | 40 | empty |
| 4 | 492 | 0.65 | 0.77 | 38 | empty |
| 5 | 95 | 0.42 | 0.77 | 16 | A4N |
Interfaces
1 interface between chains.
- A–B · 543 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5ORH · The crystal structure of CK2alpha in complex with compound 2 · the same entry in another collection · chain B against B, 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 5ORH · PDBe 5ORH · UniProt P68400
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