SMTL ID : 5orj.1

The crystal structure of CK2alpha in complex with compound 3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: N.184, D.198 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.198 MG.2: 5 residues within 4Å: Chain A: K.91, F.136, I.197, D.198 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain B: K.91, F.136, I.197, D.198 Ligands: ADP.8 No protein-ligand interaction detected (PLIP) MG.6: 6 residues within 4Å: Chain B: Y.73, K.100, D.198, G.200, L.201 Ligands: ADP.8 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: N.184, D.198 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.198

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 17 residues within 4Å: Chain A: G.71, K.72, Y.73, S.74, V.76, V.89, K.91, I.118, E.137, V.139, H.183, N.184, M.186, I.197, D.198 Ligands: MG.1, MG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.71, A:Y.73, A:S.74, A:S.74, A:E.137, A:V.139, A:D.198 Salt bridges: A:K.91, A:K.91 ADP.8: 20 residues within 4Å: Chain B: L.68, G.69, G.71, K.72, Y.73, S.74, V.76, V.89, K.91, I.118, E.137, V.139, H.183, N.184, M.186, I.197, D.198 Ligands: MG.5, MG.6, MG.7 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.71, B:G.71, B:Y.73, B:S.74, B:S.74, B:E.137, B:V.139, B:D.198, B:D.198 Water bridges: B:K.91 Salt bridges: B:K.91, B:K.91

3 x A4Q: [3-chloranyl-4-(2-ethylphenyl)phenyl]methanamine(Non-covalent)

A4Q.4: 13 residues within 4Å: Chain A: N.141, F.144, L.147, I.156, Y.159, M.160, I.163, P.182, V.185, I.187, M.244, S.247, M.248 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.144, A:L.147, A:I.156, A:Y.159, A:P.182, A:P.182, A:M.244, A:M.248 Hydrogen bonds: A:N.141, A:V.185 A4Q.9: 12 residues within 4Å: Chain B: N.141, F.144, I.156, Y.159, M.160, I.163, P.182, V.185, I.187, M.244, S.247, M.248 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.156, B:Y.159, B:P.182, B:P.182, B:I.187, B:M.244, B:M.248 Hydrogen bonds: B:N.141 Water bridges: B:N.141 A4Q.10: 10 residues within 4Å: Chain B: Q.59, D.60, Y.62, L.64, V.90, I.92, K.125, D.126, T.131, A.133 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.92, B:D.126, B:A.133 Hydrogen bonds: B:Y.62

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.11: 4 residues within 4Å: Chain B: K.252, H.257, H.259, R.267 6 PLIP interactions: 6 interactions with chain B Water bridges: B:K.252 Salt bridges: B:K.252, B:H.257, B:H.257, B:H.259, B:R.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iegre, J. et al., Second-generation CK2 alpha inhibitors targeting the alpha D pocket. Chem Sci (2018)

Release Date

2018-02-28

Peptides

Casein kinase II subunit alpha: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Casein kinase II subunit alpha

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