MolNFT v1 · #120689 · protein

Crystal structure of CK2 with compound 2

5H8B · Casein kinase II subunit alpha: “Crystal structure of CK2 with compound 2”. X-ray diffraction, 2 ligands (5Y2, SO4), 5 pockets (best druggability 0.77). MolNFT v1 #120689 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5H8B
Type: protein
Length: 662 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: 5Y2, SO4
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Casein kinase II subunit alpha (EC 2.7.11.1)	protein	331	41% helix, 15% strand	P68400

Ligands and binding sites

5Y2 · ~{N}-[5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-methyl-phenyl]ethanamide · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 12 copies · chains A, B
EDO · 1,2-ethanediol · additive · 23 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	894	0.77	0.80	77	SO4, 5Y2
2	469	0.70	0.81	52	empty
3	455	0.70	0.80	53	SO4, EDO, 5Y2
4	82	0.40	0.78	18	SO4, EDO
5	55	0.37	0.80	16	empty

Interfaces

1 interface between chains.

A–B · 521 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5H8B · Crystal structure of CK2 with compound 2 · 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 1.00

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 5H8B · PDBe 5H8B · UniProt P68400

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