SMTL ID : 5otl.1

The crystal structure of CK2alpha in complex with compound 29

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 6 residues within 4Å: Chain A: R.103, R.178, L.201, N.212, R.214, V.215 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.215 Water bridges: A:R.178 Salt bridges: A:R.103, A:R.178 ACT.2: 5 residues within 4Å: Chain A: K.91, I.118, F.136, I.197, D.198 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.136 Hydrogen bonds: A:D.198 Water bridges: A:W.199, A:W.199 Salt bridges: A:K.91 ACT.5: 5 residues within 4Å: Chain B: K.91, I.118, F.136, I.197, D.198 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.136 Hydrogen bonds: B:D.198 Water bridges: B:E.104, B:W.199 Salt bridges: B:K.91 ACT.6: 6 residues within 4Å: Chain B: R.103, R.178, L.201, N.212, R.214, V.215 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:N.212, B:V.215 Water bridges: B:R.178 Salt bridges: B:R.103, B:R.178

2 x AQT: ~{N}-[[3-chloranyl-4-(2-ethylphenyl)phenyl]methyl]-2-(5-methoxy-1~{H}-benzimidazol-2-yl)ethanamine(Non-covalent)

AQT.3: 14 residues within 4Å: Chain A: G.69, V.76, N.141, F.144, L.151, Y.159, I.163, P.182, H.183, V.185, M.186, I.187, M.244, M.248 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.144, A:L.151, A:Y.159, A:Y.159, A:V.185, A:I.187, A:M.244, A:M.248 Hydrogen bonds: A:N.141, A:V.185 AQT.7: 16 residues within 4Å: Chain B: L.68, G.69, V.76, N.141, F.144, L.151, I.156, Y.159, I.163, P.182, H.183, V.185, M.186, I.187, M.244, M.248 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.144, B:L.151, B:I.156, B:Y.159, B:Y.159, B:V.185, B:M.248 Hydrogen bonds: B:N.141, B:N.141, B:P.182 Water bridges: B:I.187

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 5 residues within 4Å: Chain A: R.218, Y.219, H.257, G.258, H.259 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.219 Salt bridges: A:R.218, A:H.257, A:H.259 PO4.8: 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 PO4.9: 4 residues within 4Å: Chain B: R.298, H.299, S.300, K.302 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.300 Water bridges: B:H.299 Salt bridges: B:H.299, B:K.302

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 6 residues within 4Å: Chain B: P.182, Y.219, F.220, S.247, E.253, P.254 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.247, B:S.247 Water bridges: B:K.181

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.11: 4 residues within 4Å: Chain B: L.225, L.226, N.261, Y.262 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.261

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
A

B
B

Casein kinase II subunit alpha

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