SMTL ID : 3r0t.1

Crystal structure of human protein kinase CK2 alpha subunit in complex with the inhibitor CX-5279

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x FU9: 3-(cyclopropylamino)-5-{[3-(trifluoromethyl)phenyl]amino}pyrimido[4,5-c]quinoline-8-carboxylic acid(Non-covalent)

FU9.1: 17 residues within 4Å: Chain A: L.45, G.46, R.47, V.53, V.66, K.68, F.113, E.114, H.115, V.116, N.118, H.160, M.163, I.174, D.175 Ligands: EDO.8, EDO.14 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.45, A:L.45, A:V.53, A:V.66, A:V.66, A:F.113, A:F.113, A:I.174, A:I.174, A:I.174 Hydrogen bonds: A:V.116, A:V.116, A:D.175 Water bridges: A:K.68, A:D.175, A:W.176, A:W.176 Salt bridges: A:K.68 pi-Stacking: A:H.160

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

SO4.2: 4 residues within 4Å: Chain A: 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:E.180, A:N.189 Salt bridges: A:R.80, A:R.155 SO4.3: 4 residues within 4Å: Chain A: R.191, K.198, N.238 Ligands: PEG.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.238, A:N.238 Salt bridges: A:R.191, A:K.198 SO4.4: 5 residues within 4Å: Chain A: D.253, R.278, R.306, Y.307, D.308 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.307, A:D.308 Water bridges: A:D.253, A:R.306, A:R.306 Salt bridges: A:R.278, A:R.306 SO4.5: 3 residues within 4Å: Chain A: N.93, K.170, R.172 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.93, A:N.93 Salt bridges: A:R.172

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

PEG.6: 5 residues within 4Å: Chain A: S.194, R.195, Y.196 Ligands: SO4.3, EDO.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.195, A:Y.196 Water bridges: A:R.195, A:R.195

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

EDO.7: 6 residues within 4Å: Chain A: Q.36, Y.39, L.41, V.101, D.103, P.104 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.36, A:Y.39 EDO.8: 6 residues within 4Å: Chain A: N.118, D.120, H.160 Ligands: FU9.1, EDO.11, EDO.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.118, A:H.160 Water bridges: A:H.160 EDO.9: 1 residues within 4Å: Chain A: D.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.37 EDO.10: 5 residues within 4Å: Chain A: K.229, F.232, F.233, V.248, F.284 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.244 EDO.11: 9 residues within 4Å: Chain A: N.118, T.119, D.120, F.121, P.159, V.162, M.163, I.164 Ligands: EDO.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.118, A:T.119, A:F.121, A:P.159, A:I.164, A:I.164 EDO.12: 5 residues within 4Å: Chain A: K.158, H.160, S.194 Ligands: PEG.6, EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.194 Water bridges: A:K.158 EDO.13: 5 residues within 4Å: Chain A: F.121, P.159, F.197, E.230 Ligands: EDO.12 No protein-ligand interaction detected (PLIP) EDO.14: 3 residues within 4Å: Chain A: N.118 Ligands: FU9.1, EDO.8 No protein-ligand interaction detected (PLIP) EDO.15: 5 residues within 4Å: Chain A: R.278, K.279, W.281, D.302, R.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.302, A:R.306 Water bridges: A:D.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Battistutta, R. et al., Unprecedented selectivity and structural determinants of a new class of protein kinase CK2 inhibitors in clinical trials for the treatment of cancer. Biochemistry (2011)

Release Date

2011-12-07

Peptides

Casein kinase II subunit alpha: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Casein kinase II subunit alpha

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