SMTL ID : 8qqb.1

Crystal structure of protein kinase CK2 catalytic subunit in complex with a Dibromo Dihydro Dibenzofuranone derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: H.290, S.291, K.293 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.290, A:S.291, A:K.293 EDO.3: 3 residues within 4Å: Chain A: D.313, D.316, K.317 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.316, A:K.317 EDO.8: 3 residues within 4Å: Chain B: H.290, S.291, K.293 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.291, B:S.291, B:K.293

2 x WJE: (4~{Z})-7,9-bis(bromanyl)-8-oxidanyl-4-(phenylazanylmethylidene)-1,2-dihydrodibenzofuran-3-one(Non-covalent)

WJE.2: 13 residues within 4Å: Chain A: L.59, S.65, V.67, V.80, K.82, I.109, F.127, E.128, V.130, N.132, M.177, I.188, D.189 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.67, A:V.80, A:I.109, A:N.132, A:I.188, A:I.188 Hydrogen bonds: A:K.82, A:K.82, A:V.130, A:V.130, A:D.189 Water bridges: A:W.190 WJE.9: 13 residues within 4Å: Chain B: L.59, S.65, V.67, V.80, K.82, I.109, F.127, E.128, V.130, N.132, M.177, I.188, D.189 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.59, B:V.67, B:V.80, B:I.109, B:N.132 Hydrogen bonds: B:K.82, B:K.82, B:V.130, B:V.130, B:D.189 Water bridges: B:W.190

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

SO4.4: 3 residues within 4Å: Chain A: R.94, R.169, N.203 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.203 Water bridges: A:R.169, A:N.203 Salt bridges: A:R.94, A:R.169 SO4.5: 3 residues within 4Å: Chain A: R.205, K.212, N.252 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.252, A:N.252 Salt bridges: A:R.205, A:K.212 SO4.6: 4 residues within 4Å: Chain A: W.38, D.39, Y.40, E.41 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.38, A:E.41, A:E.41 SO4.7: 3 residues within 4Å: Chain A: W.47, K.89, K.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.47 Salt bridges: A:K.89, A:K.116 SO4.10: 3 residues within 4Å: Chain B: R.205, K.212, N.252 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.252 Salt bridges: B:R.205, B:K.212 SO4.11: 3 residues within 4Å: Chain B: R.94, R.169, N.203 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.203 Water bridges: B:R.169 Salt bridges: B:R.94, B:R.169 SO4.12: 5 residues within 4Å: Chain B: V.45, W.47, K.89, K.93, K.116 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.93, B:K.93 Salt bridges: B:K.89, B:K.93, B:K.116 SO4.13: 4 residues within 4Å: Chain B: R.292, K.293, R.294, R.297 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.294 Salt bridges: B:R.294, B:R.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rumler, H. et al., Discovery of 7,9-Dibromo-dihydrodibenzofuran as a Potent Casein Kinase 2 (CK2) Inhibitor: Synthesis, Biological Evaluation, and Structural Studies on E-/Z-Isomers. Acs Pharmacol Transl Sci (2024)

Release Date

2024-10-16

Peptides

Casein kinase II subunit alpha: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Casein kinase II subunit alpha

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