7ZYK: Compound 9

Compound 9 Bound to CK2alpha. Determined by X-ray diffraction at 1.31 Å resolution. Released 7 Dec 2022.

Method: X-ray diffraction
Resolution: 1.31 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,112
Mol. weight: 39.96 kDa
Ligands: ADP, KEC
Released: 7 Dec 2022

Explore 7ZYK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZYK contains 28 α-helices and 10 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 28 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	15-18	4
α-helix	21-24	4
α-helix	26-28	3
α-helix	29-31	3
α-helix	36-38	3
β-strand	39-47	9	1
β-strand	51-58	8	1
β-strand	63-70	8	1
α-helix	71	1
α-helix	72-74	3
α-helix	78-88	11
β-strand	94	1	2
α-helix	95-96	2
β-strand	97-102	6	1
β-strand	109-114	6	1
α-helix	118-120	3
α-helix	121-127	7
α-helix	130-149	20
β-strand	152-153	2	3
α-helix	159-161	3
β-strand	162-165	4	2
β-strand	170-173	4	2
β-strand	180-181	2	3
α-helix	195-197	3
α-helix	200-203	4
α-helix	212-227	16
α-helix	238-249	12
α-helix	251-260	10
α-helix	267-271	5
α-helix	277-280	4
α-helix	281-284	4
α-helix	290-292	3
α-helix	295-304	10
α-helix	309-311	3
α-helix	313-314	2
α-helix	315-319	5
α-helix	322-324	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Casein kinase II subunit alpha	A	protein	328	Homo sapiens	P68400 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7ZYK_1 Casein kinase II subunit alpha (chains A)
SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITN
NEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDF
KQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEF
YHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQ
LVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFL
DKLLRYDHQSRLTAREAMEHPYFYTVVK

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
KEC	2-(5-bromanyl-6-chloranyl-1~{H}-indol-3-yl)ethanenitrile	C10 H6 Br Cl N2	1

Water and common crystallization additives (ACT) are not listed.

Primary citation

A fragment-based approach leading to the discovery of inhibitors of CK2 alpha with a novel mechanism of action. Brear, P., De Fusco, C., Atkinson, E.L. et al. RSC Med Chem (2022) 13:1420-1426. DOI 10.1039/d2md00161f · PubMed

Other PDB entries of the same protein (UniProt P68400 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3WAR 1.04 Å, Crystal structure of human CK2a
5ZN1 1.05 Å, X-ray structure of protein kinase ck2 alpha subunit in D2O
8AEC 1.09 Å, Structure of Compound 17 bound to CK2alpha
5ZN0 1.1 Å, Joint X-ray/neutron structure of protein kinase ck2 alpha subunit
7I7Y 1.15 Å, Crystal Structure of 30 bound to CK2a
6YZH 1.19 Å, Crystal structure of P8C9 bound to CK2alpha
5ZN2 1.2 Å, X-ray structure of protein kinase ck2 alpha subunit H148A mutant
7I8G 1.23 Å, Crystal Structure of 58f bound to CK2a
4KWP 1.25 Å, Crystal Structure of Human CK2-alpha in complex with a benzimidazole inhibitor (K164) at…
5CVG 1.25 Å, Crystal Structure of CK2alpha with a novel closed conformation of the aD loop
7I8P 1.25 Å, Crystal Structure of 21 bound to CK2a
7I8N 1.28 Å, Crystal Structure of 12 bound to CK2a

Browse structure collections

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