SMTL ID : 6a1c.1

Crystal structure of the CK2a1-go289 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

1 x 9NX: 5-bromanyl-2-methoxy-4-[(E)-(3-methylsulfanyl-5-phenyl-1,2,4-triazol-4-yl)iminomethyl]phenol(Non-covalent)

9NX.1: 16 residues within 4Å: Chain A: L.50, G.51, V.58, V.71, K.73, I.100, F.118, V.121, N.123, H.165, M.168, I.179, D.180 Ligands: EDO.19, EDO.20, EDO.25 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.58, A:F.118, A:I.179, A:I.179 Hydrogen bonds: A:K.73, A:D.180 Water bridges: A:K.73, A:W.181 pi-Stacking: A:H.165

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

NA.2: 5 residues within 4Å: Chain A: Q.41, D.42, Y.44 Ligands: EDO.3, EDO.4 No protein-ligand interaction detected (PLIP)

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

EDO.3: 10 residues within 4Å: Chain A: Q.41, Y.44, L.46, V.72, I.74, V.106, D.108, A.115 Ligands: NA.2, EDO.6 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: Q.41, D.42, Y.44, I.64 Ligands: NA.2, EDO.5 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: Q.41, D.42 Ligands: EDO.4 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: L.46, I.74, D.108, P.109, V.110 Ligands: EDO.3 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: G.95, G.96, P.97, N.98, I.99, R.177 Ligands: EDO.15 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: K.234, F.237, F.238, V.253, F.289 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: Y.55, L.75, K.82, I.83, E.86 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain A: N.123, T.124, P.164, V.167, M.168, I.169 Ligands: EDO.18, EDO.19 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: N.122, T.124, D.170, H.171, E.172 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: P.9, E.192, D.210, Y.211, Q.212, M.213 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: G.39, N.40, Q.41, V.106, K.107 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: N.98, E.144, R.174, K.175, L.176, R.177 Ligands: EDO.15 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: P.97, N.98, E.144, K.147 Ligands: EDO.7, EDO.14 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: Y.130, R.233, K.234, E.235 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: H.239, H.241 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: P.164, V.167, M.226, M.230 Ligands: EDO.10 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain A: N.123, P.164, H.165, V.167, M.168 Ligands: 9NX.1, EDO.10 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: G.53, K.54, Y.55, S.56, D.180 Ligands: 9NX.1 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: D.161, K.163, L.183, A.198, S.199 Ligands: EDO.23 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain A: S.199, R.200 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: R.196, V.197, A.198, K.203 Ligands: EDO.21 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: V.253, L.254, R.283, K.284, W.286, D.307 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain A: L.50, E.60, H.120, V.121, N.122, N.123 Ligands: 9NX.1 Ligand excluded by PLIP EDO.26: 1 residues within 4Å: Ligands: EDO.27 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain A: P.300, E.301, D.304, H.326, P.327 Ligands: EDO.26 Ligand excluded by PLIP EDO.28: 2 residues within 4Å: Chain A: L.208, N.243 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oshima, T. et al., Cell-based screen identifies a new potent and highly selective CK2 inhibitor for modulation of circadian rhythms and cancer cell growth. Sci Adv (2019)

Release Date

2019-03-06

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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