SMTL ID : 9fbi.1 (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 ALA- SFE- MET- VAL- 01: Cyclic peptidomimetic compound FMP37(Non-covalent)

ALA-SFE-MET-VAL-01.1: 13 residues within 4Å: Chain A: Q.51, D.52, Y.54, Q.55, L.56, V.57, R.58, F.69, I.74, V.82, I.84, V.116, A.125 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Q.51, A:Q.55, A:L.56, A:I.74, A:V.82, A:I.84 Hydrogen bonds: A:Y.54, A:Q.55, A:L.56 Water bridges: A:D.118

1 x NIO: NICOTINIC ACID(Non-covalent)

NIO.2: 10 residues within 4Å: Chain A: L.60, R.62, V.68, V.81, K.83, I.110, F.128, I.189, D.190, W.191 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.81, A:I.189 Hydrogen bonds: A:D.190 Water bridges: A:E.96, A:W.191 Salt bridges: A:K.83

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

EDO.3: 7 residues within 4Å: Chain A: D.145, R.149, R.305, H.306, L.307, V.308, S.309 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.149 Water bridges: A:R.305, A:V.308 EDO.4: 7 residues within 4Å: Chain A: F.136, P.174, S.209, Y.211, F.212, E.245, P.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.245 Water bridges: A:E.245 EDO.5: 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:H.163, A:A.330 Water bridges: A:S.227 EDO.6: 6 residues within 4Å: Chain A: F.146, D.147, F.150, Y.151, H.181, K.184 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.147, A:Y.151, A:Y.151, A:K.184 EDO.7: 7 residues within 4Å: Chain A: D.220, Y.221, Q.222, Y.276, H.277, I.278, D.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.277, A:D.279 Water bridges: A:D.220 EDO.8: 7 residues within 4Å: Chain A: K.92, R.95, R.170, L.193, E.195, N.204, V.207 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.92, A:R.95, A:R.95, A:R.170, A:N.204 Water bridges: A:R.170

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 5 residues within 4Å: Chain A: R.244, F.247, F.248, H.249, R.259 Ligand excluded by PLIP

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'

Related Entries With Identical Sequence