SMTL ID : 7at9.1

Structure of protein kinase ck2 catalytic subunit (csnk2a2 gene product) in complex with the ATP-competitive inhibitor MB002 and the alphaD-pocket ligand 3,4-dichlorophenethylamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

monomer

Ligands

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

42J.1: 14 residues within 4Å: Chain A: 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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.177, A:I.179 Hydrogen bonds: A:P.174 Water bridges: A:N.133, A:I.179 Halogen bonds: A:I.148 42J.12: 11 residues within 4Å: Chain A: L.60, G.61, V.68, N.133, K.173, H.175, N.176, M.178, I.189, D.190 Ligands: 4B0.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.189 Hydrogen bonds: A:D.190, A:D.190 Water bridges: A:N.176 Halogen bonds: A:N.133

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

CL.2: 4 residues within 4Å: Chain A: R.170, E.195, Y.203, N.204 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: R.244, V.263, F.299 Ligands: EDO.10 Ligand excluded by PLIP

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

EDO.4: 7 residues within 4Å: Chain A: L.143, I.148, S.239, M.240, R.243, E.245, L.307 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.240, A:R.243, A:R.243 EDO.5: 6 residues within 4Å: Chain A: F.146, D.147, F.150, Y.151, H.181, K.184 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.151, A:K.184 EDO.6: 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.7: 5 residues within 4Å: Chain A: E.101, L.112, I.113, D.114, T.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.112, A:D.114, A:D.114 EDO.8: 3 residues within 4Å: Chain A: Q.55, I.72, I.74 No protein-ligand interaction detected (PLIP) EDO.9: 9 residues within 4Å: Chain A: P.174, Y.211, F.212, C.235, M.236, S.239, E.245, P.246, F.247 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.239 EDO.10: 4 residues within 4Å: Chain A: K.294, N.298, F.299 Ligands: CL.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.298

1 x 4B0: 3-(4,5,6,7-tetrabromo-1H-benzotriazol-1-yl)propan-1-ol(Non-covalent)

4B0.11: 15 residues within 4Å: Chain A: L.60, V.68, V.81, K.83, I.110, F.128, E.129, Y.130, I.131, N.133, M.178, I.189, D.190, W.191 Ligands: 42J.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.83, A:D.190 Water bridges: A:W.191 Halogen bonds: A:I.131

2 x NA: SODIUM ION(Non-functional Binders)

NA.13: 5 residues within 4Å: Chain A: L.218, D.220, Y.254, D.281, F.284 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.220 NA.14: 4 residues within 4Å: Chain A: I.109, K.111, E.129, R.187 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.106, A:R.187, A:R.187 Water bridges: A:N.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lindenblatt, D. et al., Molecular Plasticity of Crystalline CK2 alpha ' Leads to KN2, a Bivalent Inhibitor of Protein Kinase CK2 with Extraordinary Selectivity. J.Med.Chem. (2022)

Release Date

2021-08-04

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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