SMTL ID : 5oqu.1

The crystal structure of CK2alpha in complex with compound 5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: R.70, G.71, K.72, S.74, V.76, V.89, K.91, I.118, E.137, V.139, H.183, N.184, M.186, I.197, D.198 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.72, A:K.72, A:E.137, A:V.139, A:D.198, A:D.198 Salt bridges: A:K.91, A:K.91 ADP.4: 17 residues within 4Å: Chain B: G.69, G.71, 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.6, MG.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.71, B:Y.73, B:S.74, B:E.137, B:V.139, B:D.198, B:D.198 Salt bridges: B:K.91, B:K.91

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: R.218, Y.219, H.257, G.258, H.259 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.218, A:H.257, A:H.259 ACT.3: 4 residues within 4Å: Chain A: R.103, R.178, Y.211, N.212 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.212 Salt bridges: A:R.103, A:R.178 ACT.8: 2 residues within 4Å: Chain B: R.267, K.270 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.267, B:K.270 ACT.9: 4 residues within 4Å: Chain B: R.103, R.178, Y.211, N.212 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:N.212 Hydrogen bonds: B:N.212 Water bridges: B:R.103 Salt bridges: B:R.103, B:R.178 ACT.10: 3 residues within 4Å: Chain B: H.299, S.300, K.302 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.300 Salt bridges: B:H.299, B:K.302

1 x A4B: [3-chloranyl-4-(2-methoxyphenyl)phenyl]methanamine(Non-covalent)

A4B.5: 10 residues within 4Å: Chain B: N.141, F.144, L.147, P.182, V.185, I.187, M.244, S.247, M.248 Ligands: CL.12 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.144, B:L.147, B:V.185, B:I.187, B:M.248 Hydrogen bonds: B:P.182

2 x MG: MAGNESIUM ION(Non-covalent)

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

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.11: 3 residues within 4Å: Chain B: K.252, H.257, H.259 4 PLIP interactions: 4 interactions with chain B Salt bridges: B:K.252, B:H.257, B:H.257, B:H.259

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

CL.12: 3 residues within 4Å: Chain B: N.141, H.183 Ligands: A4B.5 Ligand excluded by PLIP

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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