SMTL ID : 6hmb.1

STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 Gene product) IN COMPLEX WITH the inhibitor CX-4945 (Silmitasertib)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.04 Å

Oligo State

monomer

Ligands

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

EDO.1: 9 residues within 4Å: Chain A: L.100, L.103, R.104, G.105, G.106, I.109, I.110, K.111, L.112 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.100, A:G.105, A:L.112 Water bridges: A:I.109 EDO.2: 12 residues within 4Å: Chain A: N.133, T.134, D.135, F.136, L.139, Y.140, P.174, H.175, V.177, M.178, I.179 Ligands: EDO.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.133, A:T.134, A:D.135, A:D.135, A:F.136, A:I.179, A:I.179 EDO.3: 7 residues within 4Å: Chain A: K.318, L.328, E.332, A.333, E.335, H.336, P.337 No protein-ligand interaction detected (PLIP) EDO.4: 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.5: 9 residues within 4Å: Chain A: F.136, K.137, K.173, P.174, S.209, Y.211, F.212, E.245, P.246 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.137 EDO.6: 8 residues within 4Å: Chain A: N.133, D.135, F.136, H.175, M.178, I.189 Ligands: EDO.2, 3NG.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.133, A:D.135, A:D.135, A:H.175 EDO.7: 7 residues within 4Å: Chain A: R.244, P.246, F.247, F.248, H.249, R.259 Ligands: CL.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.249, A:R.259 EDO.8: 9 residues within 4Å: Chain A: K.92, R.95, R.170, G.192, L.193, N.204, R.206, V.207 Ligands: CL.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.95, A:R.95, A:R.170 Water bridges: A:N.204 EDO.9: 4 residues within 4Å: Chain A: E.202, Y.203, N.204, Q.222 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.202, A:Q.222 EDO.10: 6 residues within 4Å: Chain A: K.64, 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

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

CL.11: 4 residues within 4Å: Chain A: R.244, V.263, F.299 Ligands: EDO.7 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: R.170, E.195, Y.203, N.204 Ligands: EDO.8 Ligand excluded by PLIP

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

3NG.13: 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.6 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:E.96, A:W.191 Salt bridges: A:K.83 pi-Stacking: A:H.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lindenblatt, D. et al., Diacritic Binding of an Indenoindole Inhibitor by CK2 alpha Paralogs Explored by a Reliable Path to Atomic Resolution CK2 alpha ' Structures. Acs Omega (2019)

Release Date

2019-03-27

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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