MolNFT v1 · #170996 · protein
Crystal structure of CK2ALPHA with compound 2 bound
6YPH · Casein kinase II subunit alpha: “Crystal structure of CK2ALPHA with compound 2 bound”. X-ray diffraction, 1 ligand (N5Q), 7 pockets (best druggability 0.73). MolNFT v1 #170996 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6YPH
- Type
- protein
- Length
- 653 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
- N5Q
- Pockets
- 7 · best druggability 0.73
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 | 326 | 41% helix, 16% strand | P68400 |
| B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 327 | 41% helix, 16% strand | P68400 |
Ligands and binding sites
- N5Q · 4-[(4-naphthalen-2-yl-1,3-thiazol-2-yl)amino]-2-oxidanyl-benzoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.73 | 0.82 | 54 | N5Q |
| 2 | 788 | 0.68 | 0.75 | 69 | empty |
| 3 | 425 | 0.68 | 0.80 | 50 | N5Q |
| 4 | 94 | 0.41 | 0.77 | 23 | empty |
| 5 | 53 | 0.37 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 487 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 6YPH · PDBe 6YPH · UniProt P68400
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