Research workbench
Crystal structure of human protein kinase CK2 catalytic subunit in complex with the ATP-competitive dibenzofuran inhibitor tf (4B)
Analyse Crystal structure of human protein kinase CK2 catalytic subunit in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N9L
- Type
- protein
- Length
- 329 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
- 8QH
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 329 | 40% helix, 15% strand | P68400 |
Ligands and binding sites
- 8QH · (4~{Z})-6,7-bis(chloranyl)-4-[[(4-methylphenyl) amino]methylidene]-8-oxidanyl-1,2-dihydrodibenzofuran-3-one · ligand · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- ACT · Acetate ion · additive · 2 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 | 376 | 0.67 | 0.80 | 47 | 8QH, ACT |
| 2 | 58 | 0.30 | 0.75 | 13 | empty |
| 3 | 67 | 0.28 | 0.73 | 16 | ACT |
Compared structures
- 5N9L · Crystal structure of human Protein kinase CK2 catalytic subunit in complex with the… · 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 5N9L · PDBe 5N9L · UniProt P68400
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