SMTL ID : 5h8b.2 (1 other biounit)

Crystal structure of CK2 with compound 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: K.77, R.80, R.155, N.189, V.192 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.189 Water bridges: A:R.155, A:N.189 Salt bridges: A:K.77, A:R.80, A:R.155 SO4.2: 3 residues within 4Å: Chain A: K.229, H.234, R.244 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.229, A:H.234 Salt bridges: A:K.229, A:R.244 SO4.3: 5 residues within 4Å: Chain A: W.33, K.75, K.102 Ligands: SO4.4, EDO.13 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.31 Salt bridges: A:K.75, A:K.102 SO4.4: 3 residues within 4Å: Chain A: K.75, K.102 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.75, A:K.102 SO4.5: 4 residues within 4Å: Chain A: R.278, K.279, R.280, E.282 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.280, A:E.282, A:E.282 Salt bridges: A:R.280

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

EDO.6: 5 residues within 4Å: Chain A: W.24, D.25, Y.26, E.27, K.76 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.25, A:D.25, A:E.27, A:K.76, A:K.76 EDO.7: 3 residues within 4Å: Chain A: W.281, E.282, L.298 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.282 EDO.8: 3 residues within 4Å: Chain A: H.276, S.277, K.279 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.277, A:K.279 EDO.9: 3 residues within 4Å: Chain A: R.191, K.198, N.238 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.191, A:R.191, A:K.198, A:N.238 Water bridges: A:V.192, A:A.193 EDO.10: 4 residues within 4Å: Chain A: F.232, F.233, R.244, V.248 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.229, A:R.244 EDO.11: 4 residues within 4Å: Chain A: D.156, K.158, A.193, S.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.158 EDO.12: 4 residues within 4Å: Chain A: Y.131, D.132, F.135, R.169 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.132, A:R.169 EDO.13: 6 residues within 4Å: Chain A: V.31, K.75, I.78, K.79, P.109 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.102, A:K.102 EDO.14: 2 residues within 4Å: Chain A: D.299, K.303 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.303 EDO.15: 7 residues within 4Å: Chain A: Q.36, Y.39, L.41, V.67, D.103, P.104, A.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.36, A:Y.39, A:D.103 EDO.16: 3 residues within 4Å: Chain A: Y.196, H.234 Ligands: EDO.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.196 EDO.17: 4 residues within 4Å: Chain A: K.158, H.160, S.194 Ligands: EDO.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.194, A:S.194 EDO.18: 7 residues within 4Å: Chain A: F.121, P.159, Y.196, F.197, E.230 Ligands: EDO.16, EDO.17 No protein-ligand interaction detected (PLIP) EDO.19: 4 residues within 4Å: Chain A: R.10, S.311, L.313, E.317 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.10, A:E.317

1 x 5Y2: ~{N}-[5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-methyl-phenyl]ethanamide(Non-covalent)

5Y2.20: 15 residues within 4Å: Chain A: L.45, G.48, S.51, V.53, V.66, K.68, I.95, F.113, E.114, H.115, V.116, N.118, M.163, I.174, D.175 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.45, A:V.53, A:V.53, A:V.66, A:K.68, A:I.174, A:D.175 Hydrogen bonds: A:V.116, A:V.116, A:D.175 Water bridges: A:L.45, A:D.175, A:D.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dowling, J.E. et al., Potent and Selective CK2 Kinase Inhibitors with Effects on Wnt Pathway Signaling in Vivo. Acs Med.Chem.Lett. (2016)

Release Date

2016-02-10

Peptides

Casein kinase II subunit alpha: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Casein kinase II subunit alpha

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