SMTL ID : 8qbu.1

STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE INHIBITOR CX-4945 AND THE ALPHA-D-POCKET LIGAND 3,4-DICHLORO PHENETHYLAMINE (DPA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.09 Å

Oligo State

monomer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: K.318, L.328, E.332, A.333, E.335, H.336, P.337 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.318, A:E.332 EDO.2: 6 residues within 4Å: Chain A: F.146, D.147, F.150, Y.151, H.181, K.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.151, A:H.181, A:K.184 EDO.3: 8 residues within 4Å: Chain A: G.106, T.107, N.108, I.109, E.154, R.187 Ligands: EDO.12, EDO.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.106, A:N.108 Water bridges: A:R.187 EDO.6: 3 residues within 4Å: Chain A: K.294, N.298, F.299 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.298 EDO.7: 7 residues within 4Å: Chain A: K.173, P.174, S.209, Y.211, F.212, E.245, P.246 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain A: Y.27, A.28, E.29, V.30, L.33 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.27, A:E.29 Water bridges: A:A.28 EDO.9: 5 residues within 4Å: Chain A: D.171, K.173, L.193, A.208, S.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.171, A:K.173 EDO.10: 7 residues within 4Å: Chain A: K.92, R.95, R.170, L.193, E.195, N.204, V.207 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.95, A:R.95, A:R.170 Water bridges: A:R.170, A:E.195, A:E.195 EDO.11: 8 residues within 4Å: Chain A: V.68, D.171, K.173, H.175, N.176, I.189, D.190 Ligands: 3NG.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.176, A:N.176 Water bridges: A:K.173 EDO.12: 9 residues within 4Å: Chain A: N.108, F.150, E.154, K.184, K.185, L.186, R.187 Ligands: EDO.3, EDO.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.186, A:L.186, A:R.187 EDO.13: 6 residues within 4Å: Chain A: T.107, N.108, E.154, K.157 Ligands: EDO.3, EDO.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.154, A:K.157 EDO.14: 3 residues within 4Å: Chain A: Q.182, Q.183, K.184 No protein-ligand interaction detected (PLIP)

1 x 42J: 2-(3,4-dichlorophenyl)ethanamine(Non-covalent)

42J.4: 15 residues within 4Å: Chain A: N.133, F.136, L.143, I.148, Y.151, M.152, L.155, P.174, H.175, V.177, M.178, I.179, L.186, M.236, M.240 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.143, A:P.174, A:V.177, A:I.179 Hydrogen bonds: A:N.133 Water bridges: A:N.133, A:K.137

1 x 3NG: 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid(Non-covalent)

3NG.5: 17 residues within 4Å: Chain A: L.60, G.61, R.62, V.68, V.81, K.83, I.110, F.128, E.129, Y.130, I.131, H.175, M.178, I.189, D.190, W.191 Ligands: EDO.11 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.60, A:L.60, A:V.68, A:V.81, A:V.81, A:I.110, A:F.128, A:I.189, A:I.189, A:I.189 Hydrogen bonds: A:I.131, A:D.190 Water bridges: A:W.191, A:W.191 Salt bridges: A:K.83 pi-Stacking: A:H.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Werner, C. et al., Discovery and Exploration of Protein Kinase CK2 Binding Sites Using CK2alpha Cys336Ser as an Exquisite Crystallographic Tool. Kinases Phosphatases (2023)

Release Date

2023-12-06

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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