SMTL ID : 9fbm.1 (2 other biounits)

Structure of human protein kinase ck2 catalytic subunit (ck2alpha, csnk2a1 gene product) in complex with the cyclic peptidomimetic compound fmp37 discovered by high-throughput screening

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x ALA- SFE- MET- VAL- 01: Cyclic peptidomimetic compound FMP37(Non-covalent)

ALA-SFE-MET-VAL-01.1: 12 residues within 4Å: Chain A: Q.50, D.51, Y.53, Q.54, L.55, V.56, R.57, F.68, I.73, V.115, D.117, P.118 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Q.54, A:L.55, A:F.68, A:V.115 Hydrogen bonds: A:D.51, A:Y.53, A:Q.54, A:L.55

1 x NIO: NICOTINIC ACID(Non-covalent)

NIO.2: 6 residues within 4Å: Chain A: V.80, K.82, I.109, F.127, I.188, D.189 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.109, A:F.127, A:F.127, A:I.188, A:I.188 Hydrogen bonds: A:D.189 Water bridges: A:K.82, A:W.190 Salt bridges: A:K.82

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: R.205, K.212, N.252 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.252 Salt bridges: A:R.205, A:K.212 SO4.4: 6 residues within 4Å: Chain A: K.88, K.91, R.94, R.169, N.203, V.206 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.203 Water bridges: A:K.88, A:K.88, A:R.169, A:N.203 Salt bridges: A:K.88, A:K.91, A:R.94, A:R.169 SO4.5: 2 residues within 4Å: Chain A: R.22, P.198 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.22 SO4.6: 2 residues within 4Å: Chain A: R.33, M.164 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.160 Salt bridges: A:R.33

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

NA.7: 4 residues within 4Å: Chain A: K.89, K.90, I.92, K.93 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.90, A:I.92, A:K.93

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
A

Casein kinase II subunit alpha

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