SMTL ID : 9fbi.2 (1 other biounit)

Structure of human protein kinase ck2 catalytic subunit (ck2alpha, csnk2a2 gene product) in complex with the cyclic peptidomimetic compound fmp37 discovered by high-throughput screening

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.16 Å

Oligo State

monomer

Ligands

1 x NIO: NICOTINIC ACID(Non-covalent)

NIO.1: 11 residues within 4Å: Chain A: R.62, V.68, V.81, K.83, I.110, F.128, E.129, M.178, I.189, D.190, W.191 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.128, A:I.189, A:I.189, A:I.189 Hydrogen bonds: A:D.190 Water bridges: A:D.190, A:W.191, A:W.191 Salt bridges: A:K.83

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: F.146, D.147, F.150, Y.151, H.181, K.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.151, A:H.181, A:K.184 EDO.3: 6 residues within 4Å: Chain A: A.19, E.202, D.220, Y.221, Q.222, M.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.202, A:Q.222, A:Q.222 EDO.4: 8 residues within 4Å: Chain A: E.297, I.300, R.305, V.308, S.309, P.310, L.313 Ligands: NA.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.305 EDO.5: 6 residues within 4Å: Chain A: A.20, G.21, S.22, K.275, Y.276, Q.325 No protein-ligand interaction detected (PLIP) EDO.6: 9 residues within 4Å: Chain A: V.26, Y.27, H.163, Y.226, S.227, M.230, L.328, T.329, A.330 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.330 Water bridges: A:S.227, A:T.329 EDO.7: 4 residues within 4Å: Chain A: F.136, K.137, E.245, P.246 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.245

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 5 residues within 4Å: Chain A: R.305, H.306, V.308, S.309 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.308, A:V.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Werner, C. et al., Discovery and characterization of a novel class of cyclic peptidic compounds inhibiting the assembly of the protein kinase CK2alpha2/beta2 holoenzyme. To Be Published

Release Date

2025-06-11

Peptides

Casein kinase II subunit alpha': A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Casein kinase II subunit alpha'

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