MolNFT v1 · #126485 · protein
Complex structure of human protein kinase CK2 catalytic subunit with the inhibitor 4'-carboxy-6,8-chloro-flavonol (FLC21) crystallized under low-salt conditions
5M4F · Casein kinase II subunit alpha: “Complex structure of human protein kinase CK2 catalytic subunit with the inhibitor…”. X-ray diffraction, 2 ligands (7FC, CL), 3 pockets (best druggability 0.66). MolNFT v1 #126485 on GenesisL1: 3D…
- PDB
- 5M4F
- Type
- protein
- Length
- 330 residues
- Chains
- 1
- 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
- 7FC, CL
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 330 | 42% helix, 13% strand | P68400 |
Ligands and binding sites
- 7FC · 4-[6,8-bis(chloranyl)-3-oxidanyl-4-oxidanylidene-chromen-2-yl]benzoic acid · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.66 | 0.79 | 44 | 7FC |
| 2 | 51 | 0.37 | 0.80 | 12 | empty |
| 3 | 51 | 0.33 | 0.77 | 11 | empty |
Compared structures
- 5M4F · Complex structure of human protein kinase CK2 catalytic subunit with the inhibitor… · 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 0.98
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 5M4F · PDBe 5M4F · UniProt P68400
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