SMTL ID : 5h8e.2 (1 other biounit)

Crystal structure of CK2 with compound 7h

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

6 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: 4 residues within 4Å: Chain A: G.48, K.49, K.158 Ligands: 5Y3.23 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.49 Water bridges: A:S.51, A:K.158, A:K.158, A:K.158, A:D.175 Salt bridges: A:K.158 SO4.3: 4 residues within 4Å: Chain A: K.229, H.234, R.244 Ligands: EDO.17 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.234 Water bridges: A:K.229, A:K.229, A:H.234, A:R.244 Salt bridges: A:K.229, A:R.244 SO4.4: 4 residues within 4Å: Chain A: W.33, K.75, K.102 Ligands: SO4.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.33 Water bridges: A:K.79 Salt bridges: A:K.75, A:K.102 SO4.5: 3 residues within 4Å: Chain A: K.75, K.102 Ligands: SO4.4 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.75, A:K.102 SO4.6: 7 residues within 4Å: Chain A: H.29, V.30, V.31, E.32, I.82, E.86, I.100 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.32, A:E.32, A:E.86 Salt bridges: A:H.29

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

CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

EDO.8: 4 residues within 4Å: Chain A: W.24, D.25, Y.26, E.27 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.25, A:E.27 Water bridges: A:E.27, A:K.76, A:K.76 EDO.9: 5 residues within 4Å: Chain A: Q.36, Y.39, V.67, D.103 Ligands: EDO.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.36, A:Y.39 EDO.10: 4 residues within 4Å: Chain A: K.158, H.160, S.194, Y.196 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.160, A:S.194, A:S.194 EDO.11: 2 residues within 4Å: Chain A: S.277, R.278 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.278, A:R.278 Water bridges: A:E.252, A:R.275, A:R.275, A:S.277 EDO.12: 3 residues within 4Å: Chain A: R.278, K.279, R.280 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.280, A:R.280 Water bridges: A:R.283 EDO.13: 4 residues within 4Å: Chain A: R.191, V.192, K.198, N.238 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.191, A:K.198, A:N.238 EDO.14: 2 residues within 4Å: Chain A: R.43, K.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.44 EDO.15: 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.16: 4 residues within 4Å: Chain A: V.293, S.294, P.295, L.298 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.293 EDO.17: 6 residues within 4Å: Chain A: K.229, F.232, F.233, V.248, F.284 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.244 Water bridges: A:H.234 EDO.18: 3 residues within 4Å: Chain A: L.45, N.118 Ligands: 5Y3.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.118 EDO.19: 7 residues within 4Å: Chain A: V.11, H.148, Y.211, S.212, M.215, T.314, A.315 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.315 Water bridges: A:S.212, A:T.314, A:R.316 EDO.20: 6 residues within 4Å: Chain A: D.130, R.134, Q.290, H.291, V.293, S.294 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.130, A:R.134 Water bridges: A:V.293, A:S.294 EDO.21: 4 residues within 4Å: Chain A: Y.39, Q.40, L.41 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.41 EDO.22: 4 residues within 4Å: Chain A: T.127, D.132, H.166, R.169 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.132, A:R.169 Water bridges: A:T.127

1 x 5Y3: ~{N}-[2-[2-azanylethyl(methyl)amino]-5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]phenyl]ethanamide(Non-covalent)

5Y3.23: 19 residues within 4Å: Chain A: L.45, R.47, G.48, S.51, V.53, V.66, K.68, I.95, F.113, E.114, H.115, V.116, N.118, N.161, M.163, I.174, D.175 Ligands: SO4.2, EDO.18 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.45, A:L.45, A:V.53, A:V.66, A:K.68, A:I.174 Hydrogen bonds: A:V.116, A:V.116, A:N.161, A:N.161, A:D.175, A:D.175 Water bridges: A:K.158

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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